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/7769861/working' mkdir: created directory `/scratch/stefan/7769861/working/protonate' Storing results in /scratch/stefan/7769861/finished Working in /scratch/stefan/7769861/working /scratch/stefan/7769861/working /scratch/stefan/7769861 /scratch/stefan/7769861/working/protonate /scratch/stefan/7769861/working /scratch/stefan/7769861 Precomputing protomers for all compounds (pH: 7.4) 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 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 move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot access `/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 rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory 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 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 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 rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' mv: cannot stat `/nfs/home/stefan/.install4j_new': 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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': 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 move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file 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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot access `/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 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 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 chmod: cannot access `/nfs/home/stefan/.install4j': 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 move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: changing permissions of `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot access `/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 chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot access `/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 chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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 chmod: changing permissions of `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/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 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 mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) chmod: cannot access `/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 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 mv: cannot stat `/nfs/home/stefan/.install4j_new': 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 move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' 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: 0 protomers created Coalesing and merging protomers Protomer coalese resulted in 0 protomers Aborting! /scratch/stefan/7769861/working /scratch/stefan/7769861 /scratch/stefan/7769861 mkdir: created directory `/scratch/stefan/7769861/failed' `/scratch/stefan/7769861/working/input-smiles.ism' -> `/scratch/stefan/7769861/failed/input-smiles.ism' `/scratch/stefan/7769861/working/protonate' -> `/scratch/stefan/7769861/failed/protonate' ls: No match. ls: No match. mv: No match. mv: No match. 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/7769901/working' mkdir: created directory `/scratch/stefan/7769901/working/protonate' Storing results in /scratch/stefan/7769901/finished Working in /scratch/stefan/7769901/working /scratch/stefan/7769901/working /scratch/stefan/7769901 /scratch/stefan/7769901/working/protonate /scratch/stefan/7769901/working /scratch/stefan/7769901 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) 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 chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory chmod: cannot access `/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 Nov 28, 2019 12:34:08 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 28, 2019 12:35:08 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 28, 2019 12:36:08 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 2039 protomers created Coalesing and merging protomers 1422 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1422 protomers after new stereo-center expansion /scratch/stefan/7769901/working /scratch/stefan/7769901 Bulk generating 3D conformations all protomers in /scratch/stefan/7769901/working/3D mkdir: created directory `/scratch/stefan/7769901/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769901/working/protonate/xaaaaku-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' 1423 3D conformations generated for 1000 compounds Building REAL300000280001 mkdir: created directory `/scratch/stefan/7769901/working/building' mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280001' /scratch/stefan/7769901/working/building/REAL300000280001 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280001 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280001/0 /scratch/stefan/7769901/working/building/REAL300000280001 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1 `/scratch/stefan/7769901/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280001 none CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [36, 22, 9, 22, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 12, 12, 29, 57, 57, 16, 16, 1, 42, 42, 42, 42, 42, 22, 22, 22, 22, 1, 1, 1, 9, 16, 16, 29, 29, 16, 16, 1] 172 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 24, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 420 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280001 none CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [147, 124, 76, 124, 16, 16, 16, 16, 16, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 16, 156, 156, 156, 156, 156, 124, 124, 124, 124, 16, 16, 16, 4, 1, 1, 2, 2, 1, 1, 16] 172 rigid atoms, others: [38, 39, 42, 43, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 629 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280001 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280001/1 /scratch/stefan/7769901/working/building/REAL300000280001 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/2 `/scratch/stefan/7769901/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280001.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280001 none CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 23, 10, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 13, 29, 47, 47, 17, 17, 1, 41, 41, 41, 41, 41, 23, 23, 23, 23, 1, 1, 1, 17, 17, 29, 29, 17, 17, 1] 147 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 43, 24, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 372 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280001 none CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [136, 119, 79, 119, 17, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 142, 142, 142, 142, 142, 119, 119, 119, 119, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17] 147 rigid atoms, others: [37, 38, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43]) total number of confs: 525 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280001 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280001 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `/scratch/stefan/7769901/finished' Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280001/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280001/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280001 Building REAL300000280002 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280002' /scratch/stefan/7769901/working/building/REAL300000280002 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280002 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280002/0 /scratch/stefan/7769901/working/building/REAL300000280002 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/3 `/scratch/stefan/7769901/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCC1) `REAL300000280002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280002 none COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 65, 47, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 65, 66, 66, 66, 66, 66, 66, 66, 65, 47, 47, 6, 1, 1, 2, 2, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66] 84 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 315 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280002 none COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 1, 7, 11, 22, 22, 22, 44, 66, 66, 54, 59, 84, 84, 84, 66, 66, 1, 1, 1, 1, 1, 9, 9, 9, 7, 11, 11, 44, 66, 66, 84, 84, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [2, 36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 391 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280002 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280002 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280002/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280002 Building REAL300000280003 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280003' /scratch/stefan/7769901/working/building/REAL300000280003 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280003 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280003/0 /scratch/stefan/7769901/working/building/REAL300000280003 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/4 `/scratch/stefan/7769901/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCCC1) `REAL300000280003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280003 none COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [80, 78, 48, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 78, 81, 81, 77, 80, 80, 80, 80, 80, 78, 48, 48, 6, 1, 1, 2, 2, 1, 1, 81, 81, 81, 81, 81, 77, 81, 81, 81, 81, 81] 103 rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 397 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280003 none COC(CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 1, 7, 10, 28, 28, 28, 56, 81, 81, 71, 80, 103, 103, 103, 81, 81, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 10, 10, 56, 81, 81, 103, 103, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [2, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 427 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280003 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280003 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280003/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280003 Building REAL300000280004 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280004' /scratch/stefan/7769901/working/building/REAL300000280004 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280004 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280004/0 /scratch/stefan/7769901/working/building/REAL300000280004 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/5 `/scratch/stefan/7769901/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CCC2=CC=CC=C2)C=C1) `REAL300000280004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280004 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CCC2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 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: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 53, 14, 53, 53, 14, 14, 14, 14, 5, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 14, 14, 5, 5, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 433 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280004 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CCC2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 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: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 94, 94, 94, 94, 94, 188, 200, 201, 201, 200, 201, 201, 1, 1, 2, 2, 1, 1, 94, 94, 188, 188, 200, 200, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 43, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 723 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280004 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CCC2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 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: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 105, 94, 94, 94, 94, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 5, 8, 14, 14, 10, 14, 14, 94, 94, 94, 94, 94, 94, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 94, 94] 201 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 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: 238 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280004 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280004 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280004/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280004 Building REAL300000280005 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280005' /scratch/stefan/7769901/working/building/REAL300000280005 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280005 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280005/0 /scratch/stefan/7769901/working/building/REAL300000280005 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/6 `/scratch/stefan/7769901/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280005 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 13, 13, 9, 9, 17, 17, 17, 13, 13, 1, 1, 1, 2, 2, 2, 1, 13, 13, 17, 17, 13, 13, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 35, 22, 23, 24, 28] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280005 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 1, 13] 17 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280005 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280005 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280005/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280005 Building REAL300000280006 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280006' /scratch/stefan/7769901/working/building/REAL300000280006 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280006 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280006/0 /scratch/stefan/7769901/working/building/REAL300000280006 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/7 `/scratch/stefan/7769901/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN1CC1CC1) `REAL300000280006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280006 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 77, 77, 77, 104, 142, 142, 122, 142, 188, 196, 196, 142, 142, 20, 7, 1, 1, 1, 1, 47, 47, 47, 47, 47, 142, 142, 188, 188, 142, 142, 20, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 902 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280006 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 7, 7, 7, 15, 32, 32, 23, 32, 46, 71, 71, 32, 32, 1, 1, 1, 7, 20, 20, 5, 5, 5, 5, 5, 32, 32, 46, 46, 32, 32, 1, 7, 7, 20, 20, 20, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 36] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280006 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 32, 32, 32, 89, 142, 142, 93, 93, 93, 93, 93, 1, 1, 2, 2, 1, 1, 32, 89, 89, 142, 142, 142, 142, 142] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280006 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280006 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280006/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280006 Building REAL300000280007 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280007' /scratch/stefan/7769901/working/building/REAL300000280007 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280007 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280007/0 /scratch/stefan/7769901/working/building/REAL300000280007 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/8 `/scratch/stefan/7769901/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1) `REAL300000280007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280007 none COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 60, 60, 42, 42, 94, 105, 105, 60, 60, 1, 13, 13, 13, 2, 2, 2, 1, 60, 60, 94, 94, 60, 60] 146 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280007 none COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [115, 115, 60, 115, 60, 60, 60, 60, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 60, 115, 115, 115, 60, 60, 60, 60, 1, 1, 2, 2, 1, 1] 146 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280007 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280007 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280007/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280007 Building REAL300000280008 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280008' /scratch/stefan/7769901/working/building/REAL300000280008 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280008 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280008/0 /scratch/stefan/7769901/working/building/REAL300000280008 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/9 `/scratch/stefan/7769901/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1) `REAL300000280008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280008 none CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 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, 3, 3, 3, 9, 19, 19, 14, 18, 23, 23, 23, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 19, 19, 23, 23, 19, 19, 1, 1, 1] 35 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 42, 40, 41, 23, 24, 25, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280008 none CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 31, 19, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 19, 19, 19, 31, 31, 31, 19, 19, 19, 19, 4, 1, 1, 3, 3, 1, 1, 19, 19, 19] 35 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280008 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280008/1 /scratch/stefan/7769901/working/building/REAL300000280008 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/10 `/scratch/stefan/7769901/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1) `REAL300000280008.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280008 none CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 21, 21, 12, 9, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1] 35 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 41, 23, 24, 25, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280008 none CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 35, 21, 21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 21, 21, 21, 35, 35, 35, 21, 21, 21, 21, 1, 1, 3, 3, 1, 1, 21, 21, 21] 35 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280008 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280008 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280008/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280008/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280008 Building REAL300000280009 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280009' /scratch/stefan/7769901/working/building/REAL300000280009 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280009 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280009/0 /scratch/stefan/7769901/working/building/REAL300000280009 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/11 `/scratch/stefan/7769901/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3CC3)S2)C=C1) `REAL300000280009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280009 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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, 164, 164, 176, 176, 128, 63, 12, 63, 63, 12, 12, 12, 1, 1, 1, 1, 13, 176, 176, 176, 176, 176, 176, 13, 1, 1, 1, 1, 1, 176, 176] 176 rigid atoms, others: [15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280009 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 100, 100, 100, 100, 176, 176, 100, 1, 1, 2, 2, 1, 1, 100, 176, 176, 176, 176, 176, 1, 1] 176 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280009 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [130, 100, 130, 49, 49, 100, 100, 25, 7, 1, 6, 6, 1, 1, 1, 1, 1, 13, 13, 1, 100, 100, 100, 100, 100, 100, 1, 12, 13, 13, 13, 13, 100, 100] 176 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280009 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280009 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280009/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280009 Building REAL300000280010 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280010' /scratch/stefan/7769901/working/building/REAL300000280010 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280010 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280010/0 /scratch/stefan/7769901/working/building/REAL300000280010 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/12 `/scratch/stefan/7769901/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C) `REAL300000280010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280010 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 33, 62, 62, 17, 17, 1, 1, 1, 2, 2, 50, 50, 50, 49, 49, 29, 30, 1, 1, 9, 17, 17, 33, 33, 17, 17, 1, 2, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 43, 35, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 491 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280010 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 148, 68, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 17, 17, 25, 25, 171, 171, 171, 171, 171, 148, 148, 17, 17, 4, 1, 1, 2, 2, 1, 1, 17, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [37, 38, 41, 42, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 718 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280010 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280010 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280010/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280010 Building REAL300000280011 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280011' /scratch/stefan/7769901/working/building/REAL300000280011 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280011 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280011/0 /scratch/stefan/7769901/working/building/REAL300000280011 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/13 `/scratch/stefan/7769901/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-]) `REAL300000280011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280011 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 11, 15, 15, 15, 15, 23, 23, 23, 15, 15, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 11, 15, 15, 23, 23, 15, 15, 2, 2, 2] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280011 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 2, 2, 1, 1, 15, 15, 15] 23 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280011 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280011/1 /scratch/stefan/7769901/working/building/REAL300000280011 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/14 `/scratch/stefan/7769901/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-]) `REAL300000280011.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280011 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 15, 25, 25, 20, 20, 31, 31, 31, 25, 25, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 25, 25, 31, 31, 25, 25, 2, 2, 2] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280011 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25] 31 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280011 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280011 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280011/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280011/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280011 Building REAL300000280012 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280012' /scratch/stefan/7769901/working/building/REAL300000280012 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280012 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280012/0 /scratch/stefan/7769901/working/building/REAL300000280012 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/15 `/scratch/stefan/7769901/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1) `REAL300000280012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280012 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 7, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 25, 26, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280012 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 13, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280012 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280012/1 /scratch/stefan/7769901/working/building/REAL300000280012 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/16 `/scratch/stefan/7769901/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1) `REAL300000280012.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280012 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 38, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280012 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 17, 17, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17] 17 rigid atoms, others: [32, 33, 34, 35, 36, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280012 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280012 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280012/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280012/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280012 Building REAL300000280013 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280013' /scratch/stefan/7769901/working/building/REAL300000280013 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280013 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280013/0 /scratch/stefan/7769901/working/building/REAL300000280013 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/17 `/scratch/stefan/7769901/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280013 none CN1N=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 19, 33, 33, 26, 33, 43, 43, 43, 33, 33, 2, 2, 2, 1, 33, 33, 43, 43, 33, 33] 43 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 27] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280013 none CN1N=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 33, 33, 33, 33, 1, 1, 2, 2, 1, 1] 43 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280013 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280013 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280013/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280013 Building REAL300000280014 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280014' /scratch/stefan/7769901/working/building/REAL300000280014 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280014 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280014/0 /scratch/stefan/7769901/working/building/REAL300000280014 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/18 `/scratch/stefan/7769901/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=C2)C=C1) `REAL300000280014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 199, 201, 201, 126, 51, 31, 51, 51, 31, 31, 30, 31, 7, 1, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 201, 201, 201, 126, 31, 31, 31, 1, 1, 1, 1, 1, 31, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 34, 34, 34, 34, 34, 194, 201, 201, 194, 201, 201, 34, 1, 1, 2, 2, 1, 1, 7, 34, 34, 34, 201, 201, 194, 201, 201, 34, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 50, 17, 17, 34, 34, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 13, 31, 31, 13, 31, 31, 1, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 31, 31, 13, 31, 31, 1, 34, 34] 201 rigid atoms, others: [32, 33, 34, 40, 9, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280014 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280014/1 /scratch/stefan/7769901/working/building/REAL300000280014 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/19 `/scratch/stefan/7769901/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=C2)C=C1) `REAL300000280014.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 127, 49, 29, 49, 49, 29, 29, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 29, 201, 201, 201, 201, 201, 201, 29, 29, 29, 1, 1, 1, 1, 1, 29, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 35, 35, 35, 35, 35, 197, 201, 201, 197, 201, 201, 35, 1, 1, 2, 2, 1, 1, 35, 35, 35, 201, 201, 197, 201, 201, 35, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280014 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(SC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 17, 17, 35, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 13, 29, 29, 13, 29, 29, 1, 35, 35, 35, 35, 35, 35, 1, 1, 1, 29, 29, 13, 29, 29, 1, 35, 35] 201 rigid atoms, others: [32, 33, 39, 9, 12, 13, 14, 15, 16, 17, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280014 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280014 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280014/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280014/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280014 Building REAL300000280015 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280015' /scratch/stefan/7769901/working/building/REAL300000280015 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280015 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280015/0 /scratch/stefan/7769901/working/building/REAL300000280015 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/20 `/scratch/stefan/7769901/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2F)C=C1) `REAL300000280015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280015 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 41, 41, 41, 41, 41, 41, 41, 1, 1, 2, 2, 1, 1, 41, 41, 1, 1] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280015 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 1, 1, 41, 41] 41 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280015 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280015 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280015/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280015 Building REAL300000280016 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280016' /scratch/stefan/7769901/working/building/REAL300000280016 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280016 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280016/0 /scratch/stefan/7769901/working/building/REAL300000280016 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/21 `/scratch/stefan/7769901/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1) `REAL300000280016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280016 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280016 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 10, 11, 40, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280016 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280016/1 /scratch/stefan/7769901/working/building/REAL300000280016 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/22 `/scratch/stefan/7769901/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1) `REAL300000280016.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280016 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 10, 22, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280016 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CCC4=C3C2=CC=C4)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 40, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280016 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280016 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280016/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280016/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280016 Building REAL300000280017 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280017' /scratch/stefan/7769901/working/building/REAL300000280017 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280017 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280017/0 /scratch/stefan/7769901/working/building/REAL300000280017 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/23 `/scratch/stefan/7769901/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(F)=C1F) `REAL300000280017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280017 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 25, 31, 39, 39, 39, 31, 31, 1, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 39, 39, 31, 31] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280017 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 2, 2, 1, 1] 39 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280017 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280017 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280017/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280017 Building REAL300000280018 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280018' /scratch/stefan/7769901/working/building/REAL300000280018 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280018 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280018/0 /scratch/stefan/7769901/working/building/REAL300000280018 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/24 `/scratch/stefan/7769901/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1) `REAL300000280018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280018 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 36, 87, 87, 59, 62, 132, 134, 134, 87, 87, 1, 1, 1, 13, 13, 13, 87, 87, 132, 132, 87, 87, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280018 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 87, 152, 87, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 87, 87, 87, 152, 152, 152, 1, 1, 2, 2, 1, 1, 87, 87] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280018 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280018 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280018/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280018 Building REAL300000280019 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280019' /scratch/stefan/7769901/working/building/REAL300000280019 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280019 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280019/0 /scratch/stefan/7769901/working/building/REAL300000280019 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/25 `/scratch/stefan/7769901/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(C)C=C1OC) `REAL300000280019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280019 none CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 23, 23, 55, 81, 81, 29, 29, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 1, 13, 29, 29, 55, 55, 29, 29, 2, 2, 2, 1, 4, 4, 4] 123 rigid atoms, others: [1, 2, 3, 4, 5, 41, 19, 20, 21, 22, 23, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280019 none CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 29, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 29, 17, 17, 59, 75, 75, 75, 75, 75, 29, 6, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 59, 59, 59] 123 rigid atoms, others: [32, 33, 36, 37, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280019 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280019 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280019/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280019 Building REAL300000280020 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280020' /scratch/stefan/7769901/working/building/REAL300000280020 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280020 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280020/0 /scratch/stefan/7769901/working/building/REAL300000280020 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/26 `/scratch/stefan/7769901/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1) `REAL300000280020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280020 none CN1C=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 15, 32, 32, 21, 32, 49, 49, 49, 32, 32, 1, 2, 2, 2, 1, 32, 32, 49, 49, 32, 32] 49 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 22, 26] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280020 none CN1C=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [32, 32, 32, 32, 32, 32, 32, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 4, 4, 1, 1, 32, 32, 32, 32, 32, 1, 1, 2, 2, 1, 1] 49 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280020 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280020 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280020/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280020 Building REAL300000280021 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280021' /scratch/stefan/7769901/working/building/REAL300000280021 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280021 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280021/0 /scratch/stefan/7769901/working/building/REAL300000280021 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/27 `/scratch/stefan/7769901/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1) `REAL300000280021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280021 none CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 1, 1, 1, 1, 1, 7, 7, 7, 21, 34, 34, 34, 34, 54, 70, 70, 34, 34, 1, 1, 1, 31, 31, 31, 31, 31, 17, 17, 9, 9, 1, 34, 34, 54, 54, 34, 34, 2, 2, 2] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 21, 22, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280021 none CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 160, 127, 34, 34, 34, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 34, 34, 34, 176, 176, 176, 176, 176, 160, 160, 127, 127, 34, 1, 1, 2, 2, 1, 1, 34, 34, 34] 201 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280021 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280021 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280021/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280021 Building REAL300000280022 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280022' /scratch/stefan/7769901/working/building/REAL300000280022 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280022 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280022/0 /scratch/stefan/7769901/working/building/REAL300000280022 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/28 `/scratch/stefan/7769901/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F) `REAL300000280022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280022 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 21, 38, 38, 30, 38, 71, 95, 95, 38, 38, 1, 1, 3, 1, 1, 1, 12, 12, 12, 1, 38, 38, 71, 71, 38, 38, 3, 3, 3, 1] 170 rigid atoms, others: [2, 4, 5, 6, 7, 40, 21, 22, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280022 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [145, 145, 38, 145, 38, 38, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 38, 38, 66, 38, 38, 38, 145, 145, 145, 38, 1, 1, 2, 2, 1, 1, 66, 66, 66, 38] 170 rigid atoms, others: [32, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40]) total number of confs: 426 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280022 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280022/1 /scratch/stefan/7769901/working/building/REAL300000280022 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/29 `/scratch/stefan/7769901/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F) `REAL300000280022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280022 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 21, 43, 43, 33, 43, 80, 114, 114, 43, 43, 1, 1, 4, 1, 1, 1, 13, 13, 13, 1, 21, 43, 43, 80, 80, 43, 43, 4, 4, 4, 1] 180 rigid atoms, others: [2, 4, 5, 6, 7, 41, 21, 22, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280022 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 43, 145, 43, 43, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 43, 43, 59, 43, 43, 43, 145, 145, 145, 43, 6, 1, 1, 2, 2, 1, 1, 59, 59, 59, 43] 180 rigid atoms, others: [32, 33, 36, 37, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280022 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280022 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280022/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280022/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280022 Building REAL300000280023 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280023' /scratch/stefan/7769901/working/building/REAL300000280023 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280023 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280023/0 /scratch/stefan/7769901/working/building/REAL300000280023 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/30 `/scratch/stefan/7769901/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280023 none COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 50, 50, 50, 105, 133, 133, 116, 119, 165, 166, 166, 133, 133, 12, 12, 12, 8, 3, 3, 1, 1, 1, 1, 21, 21, 105, 133, 133, 165, 165, 133, 133] 166 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280023 none COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 15, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [107, 99, 55, 99, 129, 133, 133, 130, 133, 133, 133, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 107, 107, 107, 99, 129, 129, 133, 133, 133, 133, 55, 55, 7, 1, 1, 2, 2, 1, 1] 166 rigid atoms, others: [39, 40, 43, 44, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280023 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280023 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280023/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280023 Building REAL300000280024 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280024' /scratch/stefan/7769901/working/building/REAL300000280024 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280024 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280024/0 /scratch/stefan/7769901/working/building/REAL300000280024 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/31 `/scratch/stefan/7769901/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1) `REAL300000280024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280024 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 43, 43, 43, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280024 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 23, 28, 43, 43, 23, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 1, 43, 43] 43 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280024 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280024 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280024/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280024 Building REAL300000280025 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280025' /scratch/stefan/7769901/working/building/REAL300000280025 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280025 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280025/0 /scratch/stefan/7769901/working/building/REAL300000280025 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/32 `/scratch/stefan/7769901/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280025 none COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 42, 42, 26, 26, 62, 70, 70, 42, 42, 5, 5, 5, 1, 1, 1, 42, 42, 62, 62, 42, 42] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280025 none COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [56, 42, 42, 42, 42, 42, 42, 42, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 56, 56, 56, 42, 42, 42, 1, 1, 2, 2, 1, 1] 70 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280025 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280025/1 /scratch/stefan/7769901/working/building/REAL300000280025 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/33 `/scratch/stefan/7769901/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280025.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280025 none COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 44, 44, 35, 36, 64, 68, 68, 44, 44, 4, 4, 4, 1, 1, 1, 23, 44, 44, 64, 64, 44, 44] 68 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280025 none COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [54, 44, 44, 44, 44, 44, 44, 44, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 54, 54, 54, 44, 44, 44, 6, 1, 1, 2, 2, 1, 1] 68 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280025 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280025 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280025/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280025/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280025 Building REAL300000280026 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280026' /scratch/stefan/7769901/working/building/REAL300000280026 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280026 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280026/0 /scratch/stefan/7769901/working/building/REAL300000280026 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/34 `/scratch/stefan/7769901/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C) `REAL300000280026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280026 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 20, 14, 15, 36, 64, 64, 20, 20, 1, 1, 1, 2, 2, 22, 22, 22, 21, 22, 1, 1, 9, 20, 20, 36, 36, 20, 20, 1, 2, 3, 3, 3, 3, 3, 3] 113 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 358 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280026 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [99, 57, 12, 12, 20, 20, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 20, 20, 20, 28, 28, 99, 99, 99, 99, 99, 20, 20, 5, 1, 1, 2, 2, 1, 1, 20, 28, 28, 28, 28, 28, 28, 28] 113 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 409 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280026 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280026 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280026/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280026 Building REAL300000280027 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280027' /scratch/stefan/7769901/working/building/REAL300000280027 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280027 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280027/0 /scratch/stefan/7769901/working/building/REAL300000280027 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/35 `/scratch/stefan/7769901/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280027 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 14, 14, 29, 31, 31, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 9, 17, 17, 29, 29, 17, 17, 1] 31 rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 43, 22, 23, 24] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280027 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [27, 17, 27, 27, 17, 17, 17, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 6, 1, 1, 2, 2, 1, 1, 17] 31 rigid atoms, others: [37, 38, 41, 42, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280027 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280027/1 /scratch/stefan/7769901/working/building/REAL300000280027 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/36 `/scratch/stefan/7769901/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280027.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280027 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 15, 15, 37, 37, 37, 25, 25, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 25, 25, 37, 37, 25, 25, 1] 37 rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 42, 22, 23, 24] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280027 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 25, 37, 37, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 1, 1, 2, 2, 1, 1, 25] 37 rigid atoms, others: [36, 37, 40, 41, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280027 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280027 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280027/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280027/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280027 Building REAL300000280028 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280028' /scratch/stefan/7769901/working/building/REAL300000280028 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280028 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280028/0 /scratch/stefan/7769901/working/building/REAL300000280028 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/37 `/scratch/stefan/7769901/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280028 none N#CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 21, 21, 21, 17, 17, 1, 1, 1, 9, 17, 17, 21, 21, 17, 17, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280028 none N#CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 17, 17, 17, 6, 1, 1, 2, 2, 1, 1, 17] 21 rigid atoms, others: [11, 12, 13, 14, 15, 16, 20, 21, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 32, 22, 23, 24, 25, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280028 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280028/1 /scratch/stefan/7769901/working/building/REAL300000280028 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/38 `/scratch/stefan/7769901/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280028.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280028 none N#CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 21, 21, 21, 20, 20, 1, 1, 1, 20, 20, 21, 21, 20, 20, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280028 none N#CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 20, 20, 20, 1, 1, 2, 2, 1, 1, 20] 21 rigid atoms, others: [11, 12, 13, 14, 15, 16, 20, 21, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 27, 28, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280028 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280028 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280028/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280028/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280028 Building REAL300000280029 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280029' /scratch/stefan/7769901/working/building/REAL300000280029 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280029 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280029/0 /scratch/stefan/7769901/working/building/REAL300000280029 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/39 `/scratch/stefan/7769901/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C(F)(F)F) `REAL300000280029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280029 none CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 39, 39, 39, 39, 49, 49, 49, 39, 39, 1, 1, 2, 2, 2, 2, 2, 2, 1, 39, 39, 49, 49, 39, 39] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280029 none CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 2, 2, 1, 1] 49 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280029 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280029 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280029/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280029 Building REAL300000280030 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280030' /scratch/stefan/7769901/working/building/REAL300000280030 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280030 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280030/0 /scratch/stefan/7769901/working/building/REAL300000280030 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/40 `/scratch/stefan/7769901/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=NC=C23)C=C1) `REAL300000280030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280030 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=NC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280030 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=NC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 45, 47, 53, 53, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280030 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280030/1 /scratch/stefan/7769901/working/building/REAL300000280030 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/41 `/scratch/stefan/7769901/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=NC=NC=C23)C=C1) `REAL300000280030.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280030 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=NC=NC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280030 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=NC=NC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 50, 53, 53, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280030 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280030 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280030/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280030/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280030 Building REAL300000280031 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280031' /scratch/stefan/7769901/working/building/REAL300000280031 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280031 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280031/0 /scratch/stefan/7769901/working/building/REAL300000280031 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/42 `/scratch/stefan/7769901/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC=CC=C23)C=C1) `REAL300000280031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280031 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 2, 2, 1, 1, 55, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280031 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 47, 47, 55, 55, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280031 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280031/1 /scratch/stefan/7769901/working/building/REAL300000280031 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/43 `/scratch/stefan/7769901/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC=CC=C23)C=C1) `REAL300000280031.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280031 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 11, 52, 52, 52, 52, 52, 52, 1, 1] 52 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280031 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 25, 1, 1, 1, 1, 1, 1, 52, 52] 52 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280031 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280031 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280031/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280031/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280031 Building REAL300000280032 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280032' /scratch/stefan/7769901/working/building/REAL300000280032 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280032 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280032/0 /scratch/stefan/7769901/working/building/REAL300000280032 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/44 `/scratch/stefan/7769901/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280032 none CN1N=C2CCCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 11, 11, 11, 23, 38, 38, 30, 38, 59, 59, 59, 38, 38, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 59, 59, 38, 38] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 33, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280032 none CN1N=C2CCCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 4, 4, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1] 59 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280032 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280032/1 /scratch/stefan/7769901/working/building/REAL300000280032 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/45 `/scratch/stefan/7769901/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280032.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280032 none CN1N=C2CCCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 29, 29, 25, 29, 53, 53, 53, 29, 29, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 21, 29, 29, 53, 53, 29, 29] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 33, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280032 none CN1N=C2CCCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 2, 2, 1, 1] 53 rigid atoms, others: [36, 37, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280032 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280032 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280032/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280032/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280032 Building REAL300000280033 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280033' /scratch/stefan/7769901/working/building/REAL300000280033 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280033 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280033/0 /scratch/stefan/7769901/working/building/REAL300000280033 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/46 `/scratch/stefan/7769901/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(C)(C)C)=N1) `REAL300000280033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280033 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 11, 11, 11, 11, 15, 15, 15, 11, 11, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 11, 11, 15, 15, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280033 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 15 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280033 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280033 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280033/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280033 Building REAL300000280034 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280034' /scratch/stefan/7769901/working/building/REAL300000280034 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280034 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280034/0 /scratch/stefan/7769901/working/building/REAL300000280034 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/47 `/scratch/stefan/7769901/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCC3)N=C2)C=C1) `REAL300000280034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280034 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 105, 101, 108, 108, 70, 23, 12, 23, 23, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 108, 108, 108, 108, 108, 108, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 108, 108] 108 rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 39, 40]) total number of confs: 260 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280034 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 42, 42, 42, 108, 108, 108, 108, 42, 42, 1, 1, 2, 2, 1, 1, 42, 108, 108, 108, 108, 108, 108, 108, 108, 108, 42, 1, 1] 108 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 316 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280034 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [52, 42, 52, 17, 17, 42, 42, 9, 2, 1, 2, 2, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 42, 42, 42, 42, 42, 42, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 42, 42] 108 rigid atoms, others: [38, 9, 12, 13, 14, 15, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 291 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280034 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280034 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280034/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280034 Building REAL300000280035 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280035' /scratch/stefan/7769901/working/building/REAL300000280035 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280035 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280035/0 /scratch/stefan/7769901/working/building/REAL300000280035 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/48 `/scratch/stefan/7769901/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Br)=N1) `REAL300000280035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280035 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 20, 34, 34, 27, 27, 38, 38, 38, 34, 34, 1, 1, 1, 2, 2, 2, 1, 34, 34, 38, 38, 34, 34] 38 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280035 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [34, 34, 34, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 34, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 1, 1] 38 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280035 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280035 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280035/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280035 Building REAL300000280036 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280036' /scratch/stefan/7769901/working/building/REAL300000280036 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280036 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280036/0 /scratch/stefan/7769901/working/building/REAL300000280036 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/49 `/scratch/stefan/7769901/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2(COCC3=CC=CC=C3)CC2)C=C1) `REAL300000280036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280036 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2(COCC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 174, 167, 110, 167, 167, 43, 17, 4, 1, 1, 1, 1, 1, 1, 1, 110, 110, 201, 201, 201, 201, 201, 201, 174, 43, 43, 4, 4, 1, 1, 1, 1, 1, 110, 110, 110, 110, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 729 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280036 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2(COCC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 18, 48, 100, 201, 201, 201, 201, 201, 201, 18, 18, 1, 1, 2, 2, 1, 1, 7, 48, 48, 201, 201, 201, 201, 201, 201, 201, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 44, 45, 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]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280036 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2(COCC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 30, 15, 15, 18, 18, 9, 4, 1, 4, 4, 1, 1, 7, 18, 69, 110, 110, 91, 110, 110, 1, 1, 18, 18, 18, 18, 18, 18, 9, 7, 7, 69, 69, 110, 110, 110, 110, 110, 1, 1, 1, 1, 18, 18] 201 rigid atoms, others: [40, 9, 42, 43, 12, 13, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280036 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280036 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280036/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280036 Building REAL300000280037 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280037' /scratch/stefan/7769901/working/building/REAL300000280037 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280037 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280037/0 /scratch/stefan/7769901/working/building/REAL300000280037 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/50 `/scratch/stefan/7769901/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2[O-])C=C1) `REAL300000280037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280037 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 1, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280037 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 15, 15] 15 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280037 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280037/1 /scratch/stefan/7769901/working/building/REAL300000280037 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/51 `/scratch/stefan/7769901/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2O)C=C1) `REAL300000280037.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280037 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 1, 1, 2, 2, 1, 1, 45, 45, 45, 90, 1, 1] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280037 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [45, 45, 45, 41, 42, 45, 45, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 1, 1, 1, 2, 45, 45] 90 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280037 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280037 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280037/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280037/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280037 Building REAL300000280038 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280038' /scratch/stefan/7769901/working/building/REAL300000280038 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280038 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280038/0 /scratch/stefan/7769901/working/building/REAL300000280038 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/52 `/scratch/stefan/7769901/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280038 none C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 19, 21, 56, 64, 64, 29, 29, 1, 1, 15, 15, 15, 7, 7, 3, 3, 1, 1, 9, 29, 29, 56, 56, 29, 29, 1, 1] 164 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280038 none C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [136, 101, 51, 15, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 136, 136, 136, 101, 101, 51, 51, 29, 29, 6, 1, 1, 2, 2, 1, 1, 29, 29] 164 rigid atoms, others: [34, 35, 38, 39, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280038 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280038 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280038/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280038 Building REAL300000280039 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280039' /scratch/stefan/7769901/working/building/REAL300000280039 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280039 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280039/0 /scratch/stefan/7769901/working/building/REAL300000280039 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/53 `/scratch/stefan/7769901/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280039 none COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 36, 85, 85, 52, 85, 138, 139, 139, 85, 85, 12, 12, 12, 1, 1, 85, 85, 138, 138, 85, 85] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280039 none COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [149, 149, 85, 149, 85, 85, 85, 85, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 149, 149, 149, 85, 85, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280039 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280039 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280039/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280039 Building REAL300000280040 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280040' /scratch/stefan/7769901/working/building/REAL300000280040 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280040 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280040/0 /scratch/stefan/7769901/working/building/REAL300000280040 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/54 `/scratch/stefan/7769901/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280040 none CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 57, 57, 57, 57, 81, 85, 85, 57, 57, 5, 5, 5, 5, 5, 2, 2, 2, 1, 57, 57, 81, 81, 57, 57] 105 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280040 none CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [93, 57, 57, 57, 57, 57, 57, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 93, 93, 93, 93, 93, 57, 57, 57, 57, 1, 1, 2, 2, 1, 1] 105 rigid atoms, others: [32, 35, 36, 11, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280040 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280040 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280040/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280040 Building REAL300000280041 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280041' /scratch/stefan/7769901/working/building/REAL300000280041 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280041 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280041/0 /scratch/stefan/7769901/working/building/REAL300000280041 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/55 `/scratch/stefan/7769901/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280041 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 15, 15, 40, 52, 52, 22, 22, 1, 1, 1, 11, 11, 11, 1, 1, 9, 22, 22, 40, 40, 22, 22, 1] 74 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280041 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [70, 22, 70, 22, 22, 22, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 22, 22, 22, 70, 70, 70, 22, 22, 6, 1, 1, 2, 2, 1, 1, 22] 74 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280041 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280041/1 /scratch/stefan/7769901/working/building/REAL300000280041 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/56 `/scratch/stefan/7769901/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280041.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280041 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 15, 15, 43, 49, 49, 25, 25, 1, 1, 1, 11, 11, 11, 1, 1, 25, 25, 43, 43, 25, 25, 1] 73 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280041 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [71, 25, 71, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 25, 25, 25, 71, 71, 71, 25, 25, 1, 1, 2, 2, 1, 1, 25] 73 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280041 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280041 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280041/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280041/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280041 Building REAL300000280042 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280042' /scratch/stefan/7769901/working/building/REAL300000280042 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280042 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280042/0 /scratch/stefan/7769901/working/building/REAL300000280042 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/57 `/scratch/stefan/7769901/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280042 none NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 11, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 23, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280042 none NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 1, 13] 13 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 26, 27, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280042 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280042/1 /scratch/stefan/7769901/working/building/REAL300000280042 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/58 `/scratch/stefan/7769901/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280042.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280042 none NC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 7, 9, 9, 8, 9, 13, 13, 13, 9, 9, 1, 1, 1, 1, 1, 7, 9, 9, 13, 13, 9, 9, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280042 none NC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 7, 7, 7, 7, 7, 4, 1, 1, 2, 2, 1, 1, 7] 13 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280042 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280042 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280042/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280042/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280042 Building REAL300000280043 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280043' /scratch/stefan/7769901/working/building/REAL300000280043 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280043 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280043/0 /scratch/stefan/7769901/working/building/REAL300000280043 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/59 `/scratch/stefan/7769901/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(F)F)=C2)C=C1) `REAL300000280043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280043 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 41, 41, 23, 23, 41, 41, 68, 68, 41, 1, 1, 2, 2, 1, 1, 11, 41, 41, 68, 41, 1, 1] 68 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280043 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 17, 17, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 41, 41, 41, 41, 41, 41, 9, 1, 1, 12, 1, 41, 41] 68 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 33, 34]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280043 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280043/1 /scratch/stefan/7769901/working/building/REAL300000280043 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/60 `/scratch/stefan/7769901/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(F)F)=C2)C=C1) `REAL300000280043.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280043 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 77, 77, 45, 1, 1, 2, 2, 1, 1, 45, 45, 77, 45, 1, 1] 77 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280043 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [51, 45, 51, 17, 17, 45, 45, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 45, 45, 45, 45, 45, 45, 1, 1, 12, 1, 45, 45] 77 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 30, 32, 33]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280043 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280043 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280043/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280043/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280043 Building REAL300000280044 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280044' /scratch/stefan/7769901/working/building/REAL300000280044 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280044 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280044/0 /scratch/stefan/7769901/working/building/REAL300000280044 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/61 `/scratch/stefan/7769901/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=NS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC=C1) `REAL300000280044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280044 none CN(C)S(=O)(=NS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', '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, 14, 11, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [114, 65, 114, 65, 65, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 65, 130, 130, 72, 130, 130, 114, 114, 114, 114, 114, 114, 7, 1, 1, 2, 2, 1, 1, 130, 130, 85, 130, 130] 153 rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280044 none CN(C)S(=O)(=NS(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', '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, 14, 11, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 1, 6, 6, 6, 39, 39, 39, 84, 130, 130, 107, 116, 153, 153, 153, 130, 130, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 84, 130, 130, 153, 153, 130, 130, 1, 1, 1, 1, 1] 153 rigid atoms, others: [3, 39, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280044 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280044 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280044/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280044 Building REAL300000280045 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280045' /scratch/stefan/7769901/working/building/REAL300000280045 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280045 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280045/0 /scratch/stefan/7769901/working/building/REAL300000280045 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/62 `/scratch/stefan/7769901/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Cl)=C2)C=C1) `REAL300000280045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280045 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 103, 103, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 9, 103, 103, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 445 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280045 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 193, 201, 201, 141, 70, 11, 70, 70, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 141, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 610 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280045 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280045 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280045/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280045 Building REAL300000280046 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280046' /scratch/stefan/7769901/working/building/REAL300000280046 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280046 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280046/0 /scratch/stefan/7769901/working/building/REAL300000280046 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/63 `/scratch/stefan/7769901/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1CC) `REAL300000280046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280046 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 11, 11, 21, 32, 32, 13, 13, 1, 1, 1, 5, 35, 36, 36, 35, 35, 24, 24, 1, 1, 9, 13, 13, 21, 21, 13, 13, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 42, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280046 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 40, 13, 7, 13, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 13, 13, 13, 33, 110, 110, 110, 110, 110, 95, 95, 13, 13, 4, 1, 1, 2, 2, 1, 1, 13, 33, 33, 33, 33, 33] 201 rigid atoms, others: [36, 37, 40, 41, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280046 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280046 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280046/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280046 Building REAL300000280047 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280047' /scratch/stefan/7769901/working/building/REAL300000280047 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280047 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280047/0 /scratch/stefan/7769901/working/building/REAL300000280047 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/64 `/scratch/stefan/7769901/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280047 none N#CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [8, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 27, 27, 27, 17, 17, 1, 1, 7, 7, 3, 3, 1, 1, 9, 17, 17, 27, 27, 17, 17, 1, 1] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 38, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280047 none N#CCCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [8, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 27, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 17, 17, 53, 53, 27, 27, 17, 17, 4, 1, 1, 2, 2, 1, 1, 17, 17] 55 rigid atoms, others: [32, 35, 36, 11, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280047 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280047/1 /scratch/stefan/7769901/working/building/REAL300000280047 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/65 `/scratch/stefan/7769901/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280047.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280047 none N#CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [8, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 13, 13, 29, 29, 29, 19, 19, 1, 1, 5, 5, 3, 3, 1, 1, 19, 19, 29, 29, 19, 19, 1, 1] 43 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 36, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280047 none N#CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [8, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 11, 19, 19, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 19, 19, 43, 43, 29, 29, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19] 43 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280047 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280047 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280047/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280047/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280047 Building REAL300000280048 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280048' /scratch/stefan/7769901/working/building/REAL300000280048 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280048 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280048/0 /scratch/stefan/7769901/working/building/REAL300000280048 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/66 `/scratch/stefan/7769901/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280048 none CC1=CC(Cl)=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 7, 12, 12, 12, 7, 7, 2, 2, 2, 1, 1, 2, 2, 2, 5, 7, 7, 12, 12, 7, 7] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280048 none CC1=CC(Cl)=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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 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, 3, 3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 2, 2, 1, 1] 5 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280048 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280048 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280048/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280048 Building REAL300000280049 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280049' /scratch/stefan/7769901/working/building/REAL300000280049 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280049 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280049/0 /scratch/stefan/7769901/working/building/REAL300000280049 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/67 `/scratch/stefan/7769901/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280049 none COC1=NSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 39, 39, 30, 30, 53, 55, 55, 39, 39, 1, 3, 3, 3, 39, 39, 53, 53, 39, 39, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280049 none COC1=NSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [47, 39, 39, 39, 39, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 39, 47, 47, 47, 1, 1, 2, 2, 1, 1, 39] 61 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 26, 27, 30]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280049 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280049 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280049/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280049 Building REAL300000280050 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280050' /scratch/stefan/7769901/working/building/REAL300000280050 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280050 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280050/0 /scratch/stefan/7769901/working/building/REAL300000280050 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/68 `/scratch/stefan/7769901/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280050 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 1, 1, 1, 7, 7, 7, 15, 29, 29, 20, 20, 49, 51, 51, 29, 29, 4, 4, 4, 1, 1, 9, 9, 9, 9, 9, 9, 1, 29, 29, 49, 49, 29, 29] 64 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280050 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 29, 29, 29, 29, 29, 29, 49, 49, 51, 51, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 41, 41, 41, 29, 29, 51, 51, 51, 51, 51, 51, 29, 1, 1, 2, 2, 1, 1] 64 rigid atoms, others: [39, 40, 43, 44, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 173 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280050 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280050/1 /scratch/stefan/7769901/working/building/REAL300000280050 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/69 `/scratch/stefan/7769901/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280050.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280050 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 1, 1, 1, 7, 7, 7, 15, 25, 25, 21, 20, 33, 36, 36, 25, 25, 4, 4, 4, 1, 1, 9, 9, 9, 9, 9, 9, 1, 15, 25, 25, 33, 33, 25, 25] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280050 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 25, 25, 25, 25, 25, 37, 37, 37, 37, 25, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 30, 30, 30, 25, 25, 37, 37, 37, 37, 37, 37, 25, 6, 1, 1, 2, 2, 1, 1] 43 rigid atoms, others: [40, 41, 44, 45, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280050 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280050 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280050/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280050/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280050 Building REAL300000280051 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280051' /scratch/stefan/7769901/working/building/REAL300000280051 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280051 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280051/0 /scratch/stefan/7769901/working/building/REAL300000280051 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/70 `/scratch/stefan/7769901/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)O1) `REAL300000280051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280051 none CC1(C)CCCC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 71, 115, 115, 115, 115, 145, 145, 145, 115, 115, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 71, 115, 115, 145, 145, 115, 115] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 35, 22, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280051 none CC1(C)CCCC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 67, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 67, 67, 6, 1, 1, 2, 2, 1, 1] 145 rigid atoms, others: [43, 39, 40, 44, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280051 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280051 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280051/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280051 Building REAL300000280052 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280052' /scratch/stefan/7769901/working/building/REAL300000280052 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280052 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280052/0 /scratch/stefan/7769901/working/building/REAL300000280052 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/71 `/scratch/stefan/7769901/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Cl)C=C1) `REAL300000280052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280052 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 150, 150, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 12, 150, 150, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 486 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280052 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 181, 201, 201, 134, 60, 9, 60, 60, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 134, 9, 9, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 658 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280052 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280052 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280052/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280052 Building REAL300000280053 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280053' /scratch/stefan/7769901/working/building/REAL300000280053 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280053 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280053/0 /scratch/stefan/7769901/working/building/REAL300000280053 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/72 `/scratch/stefan/7769901/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280053 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 23, 43, 43, 33, 34, 57, 57, 57, 43, 43, 3, 3, 3, 1, 1, 1, 43, 43, 57, 57, 43, 43] 57 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 28, 29, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280053 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [43, 43, 43, 43, 31, 43, 43, 43, 43, 43, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1] 57 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280053 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280053/1 /scratch/stefan/7769901/working/building/REAL300000280053 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/73 `/scratch/stefan/7769901/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280053.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280053 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 25, 43, 43, 35, 35, 51, 53, 53, 43, 43, 4, 4, 4, 1, 1, 1, 25, 43, 43, 51, 51, 43, 43] 53 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 28, 29, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280053 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [47, 43, 43, 43, 31, 43, 43, 43, 43, 43, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 47, 47, 47, 43, 43, 43, 6, 1, 1, 2, 2, 1, 1] 53 rigid atoms, others: [32, 33, 36, 37, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280053 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280053 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280053/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280053/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280053 Building REAL300000280054 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280054' /scratch/stefan/7769901/working/building/REAL300000280054 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280054 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280054/0 /scratch/stefan/7769901/working/building/REAL300000280054 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/74 `/scratch/stefan/7769901/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1) `REAL300000280054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280054 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 19, 43, 43, 28, 28, 59, 59, 59, 43, 43, 1, 1, 1, 4, 4, 1, 2, 2, 2, 43, 43, 59, 59, 43, 43, 1, 4, 4] 85 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280054 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 43, 43, 43, 65, 65, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1, 43, 65, 65] 85 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280054 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280054/1 /scratch/stefan/7769901/working/building/REAL300000280054 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/75 `/scratch/stefan/7769901/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1) `REAL300000280054.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280054 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 15, 27, 27, 23, 23, 43, 45, 45, 27, 27, 1, 1, 1, 4, 4, 1, 2, 2, 2, 15, 27, 27, 43, 43, 27, 27, 1, 4, 4] 58 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280054 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 27, 27, 27, 44, 44, 27, 27, 27, 27, 6, 1, 1, 2, 2, 1, 1, 27, 44, 44] 58 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 15, 16, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280054 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280054 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280054/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280054/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280054 Building REAL300000280055 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280055' /scratch/stefan/7769901/working/building/REAL300000280055 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280055 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280055/0 /scratch/stefan/7769901/working/building/REAL300000280055 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/76 `/scratch/stefan/7769901/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280055 none CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 27, 27, 20, 20, 50, 73, 73, 27, 27, 10, 10, 10, 10, 10, 5, 6, 1, 1, 1, 1, 13, 27, 27, 50, 50, 27, 27] 91 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280055 none CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [58, 53, 27, 27, 27, 27, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 58, 58, 58, 58, 58, 53, 53, 27, 27, 27, 27, 6, 1, 1, 2, 2, 1, 1] 91 rigid atoms, others: [35, 36, 39, 40, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280055 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280055/1 /scratch/stefan/7769901/working/building/REAL300000280055 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/77 `/scratch/stefan/7769901/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280055.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280055 none CCCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 24, 24, 56, 73, 73, 32, 32, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 32, 32, 56, 56, 32, 32] 93 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280055 none CCCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [65, 61, 32, 32, 32, 32, 32, 32, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 65, 65, 65, 65, 65, 61, 61, 32, 32, 32, 32, 1, 1, 2, 2, 1, 1] 93 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280055 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280055 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280055/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280055/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280055 Building REAL300000280056 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280056' /scratch/stefan/7769901/working/building/REAL300000280056 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280056 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280056/0 /scratch/stefan/7769901/working/building/REAL300000280056 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/78 `/scratch/stefan/7769901/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)F)C=C1) `REAL300000280056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280056 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 75, 75, 75, 75, 75, 75, 75, 1, 1, 2, 2, 1, 1, 75, 75, 75, 1, 1] 75 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280056 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 37, 37, 75, 75, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 75, 75, 75, 75, 75, 75, 1, 1, 5, 75, 75] 75 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280056 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280056/1 /scratch/stefan/7769901/working/building/REAL300000280056 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/79 `/scratch/stefan/7769901/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC=C2C(F)F)C=C1) `REAL300000280056.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280056 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 62, 62, 62, 62, 62, 74, 74, 1, 1, 2, 2, 1, 1, 11, 62, 62, 74, 1, 1] 74 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280056 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [64, 62, 64, 25, 25, 62, 62, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 62, 62, 62, 62, 62, 62, 13, 1, 1, 6, 62, 62] 74 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280056 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280056 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280056/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280056/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280056 Building REAL300000280057 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280057' /scratch/stefan/7769901/working/building/REAL300000280057 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280057 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280057/0 /scratch/stefan/7769901/working/building/REAL300000280057 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/80 `/scratch/stefan/7769901/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1) `REAL300000280057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280057 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 2, 2, 1, 1, 36, 1, 1] 36 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280057 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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, 34, 36, 36, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 36, 36, 1, 36, 36] 36 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280057 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280057 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280057/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280057 Building REAL300000280058 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280058' /scratch/stefan/7769901/working/building/REAL300000280058 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280058 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280058/0 /scratch/stefan/7769901/working/building/REAL300000280058 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/81 `/scratch/stefan/7769901/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280058 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 41, 125, 152, 152, 145, 152, 152, 41, 41, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 41, 41, 41, 125, 125, 152, 152, 152, 152, 152, 41, 41, 41, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [41, 42, 45, 46, 17, 18, 19, 20, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 523 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280058 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 15, 15, 10, 15, 15, 1, 1, 1, 1, 10, 10, 10, 20, 41, 41, 30, 30, 63, 79, 79, 41, 41, 2, 2, 2, 7, 7, 15, 15, 15, 15, 15, 2, 2, 2, 41, 41, 63, 63, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 394 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280058 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 66, 66, 66, 117, 152, 152, 141, 141, 201, 201, 201, 152, 152, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 15, 15, 15, 152, 152, 201, 201, 152, 152] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 759 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280058 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280058 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280058/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280058 Building REAL300000280059 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280059' /scratch/stefan/7769901/working/building/REAL300000280059 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280059 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280059/0 /scratch/stefan/7769901/working/building/REAL300000280059 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/82 `/scratch/stefan/7769901/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1) `REAL300000280059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280059 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 7, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 22, 23, 36, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280059 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 17, 17, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 17, 17] 17 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280059 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280059/1 /scratch/stefan/7769901/working/building/REAL300000280059 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/83 `/scratch/stefan/7769901/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1) `REAL300000280059.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280059 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280059 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CC=NC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 18, 19, 21, 21, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 22, 23, 24, 25, 26, 27]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280059 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280059 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280059/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280059/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280059 Building REAL300000280060 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280060' /scratch/stefan/7769901/working/building/REAL300000280060 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280060 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280060/0 /scratch/stefan/7769901/working/building/REAL300000280060 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/84 `/scratch/stefan/7769901/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280060 none COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 18, 19, 49, 51, 51, 31, 31, 1, 9, 9, 9, 1, 2, 2, 2, 31, 31, 49, 49, 31, 31, 1] 81 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 27, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280060 none COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [63, 63, 31, 63, 31, 31, 31, 31, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 31, 63, 63, 63, 31, 31, 31, 31, 1, 1, 2, 2, 1, 1, 31] 81 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280060 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280060/1 /scratch/stefan/7769901/working/building/REAL300000280060 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/85 `/scratch/stefan/7769901/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280060.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280060 none COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 31, 31, 25, 24, 49, 53, 53, 31, 31, 1, 13, 13, 13, 1, 2, 2, 2, 17, 31, 31, 49, 49, 31, 31, 1] 89 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 23, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280060 none COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 31, 71, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 31, 71, 71, 71, 31, 31, 31, 31, 6, 1, 1, 2, 2, 1, 1, 31] 89 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280060 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280060 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280060/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280060/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280060 Building REAL300000280061 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280061' /scratch/stefan/7769901/working/building/REAL300000280061 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280061 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280061/0 /scratch/stefan/7769901/working/building/REAL300000280061 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/86 `/scratch/stefan/7769901/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1F) `REAL300000280061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280061 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 23, 35, 35, 30, 29, 41, 41, 41, 35, 35, 1, 1, 1, 1, 1, 35, 35, 41, 41, 35, 35] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280061 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 35, 35, 35, 35, 35, 1, 1, 2, 2, 1, 1] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280061 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280061 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280061/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280061 Building REAL300000280062 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280062' /scratch/stefan/7769901/working/building/REAL300000280062 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280062 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280062/0 /scratch/stefan/7769901/working/building/REAL300000280062 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/87 `/scratch/stefan/7769901/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280062 none COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 69, 69, 40, 40, 102, 108, 108, 69, 69, 1, 5, 5, 5, 69, 69, 102, 102, 69, 69, 1] 139 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280062 none COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [116, 116, 69, 116, 69, 69, 69, 69, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 69, 116, 116, 116, 1, 1, 2, 2, 1, 1, 69] 139 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280062 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280062 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280062/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280062 Building REAL300000280063 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280063' /scratch/stefan/7769901/working/building/REAL300000280063 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280063 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280063/0 /scratch/stefan/7769901/working/building/REAL300000280063 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/88 `/scratch/stefan/7769901/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280063 none CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 11, 11, 17, 17, 17, 13, 13, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 9, 13, 13, 17, 17, 13, 13, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 45, 11, 35, 25, 36, 26, 37] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280063 none CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 2, 2, 1, 1, 13] 17 rigid atoms, others: [39, 40, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280063 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280063/1 /scratch/stefan/7769901/working/building/REAL300000280063 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/89 `/scratch/stefan/7769901/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280063.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280063 none CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 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', 'S.o2', 'O.2', 'O.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 13, 13, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 34, 11, 35, 25, 36, 26, 37] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280063 none CC1(C)CC(=O)NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 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', 'S.o2', 'O.2', 'O.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21] 21 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280063 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280063 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280063/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280063/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280063 Building REAL300000280064 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280064' /scratch/stefan/7769901/working/building/REAL300000280064 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280064 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280064/0 /scratch/stefan/7769901/working/building/REAL300000280064 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/90 `/scratch/stefan/7769901/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280064 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 16, 16, 35, 53, 53, 23, 23, 1, 1, 14, 14, 14, 13, 13, 1, 1, 1, 1, 1, 1, 9, 23, 23, 35, 35, 23, 23, 1] 81 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 45, 25, 36, 26, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280064 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 57, 23, 57, 23, 23, 23, 23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 23, 23, 81, 81, 81, 81, 81, 23, 23, 23, 23, 23, 23, 6, 1, 1, 2, 2, 1, 1, 23] 81 rigid atoms, others: [39, 40, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280064 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280064/1 /scratch/stefan/7769901/working/building/REAL300000280064 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/91 `/scratch/stefan/7769901/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280064.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280064 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 27, 33, 33, 17, 17, 1, 1, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 27, 27, 17, 17, 1] 59 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 44, 34, 25, 36, 26, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280064 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 45, 17, 45, 17, 17, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 17, 17, 57, 57, 57, 57, 57, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17] 59 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280064 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280064 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280064/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280064/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280064 Building REAL300000280065 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280065' /scratch/stefan/7769901/working/building/REAL300000280065 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280065 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280065/0 /scratch/stefan/7769901/working/building/REAL300000280065 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/92 `/scratch/stefan/7769901/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCC3)N=C2)C=C1) `REAL300000280065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280065 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 119, 119, 57, 20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 1, 11, 11, 119, 119, 119, 119, 119, 119, 11, 1, 1, 1, 1, 1, 1, 1, 11, 119, 119] 119 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280065 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 51, 51, 51, 119, 119, 119, 51, 51, 1, 1, 1, 1, 1, 1, 51, 119, 119, 119, 119, 119, 119, 119, 51, 1, 1] 119 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 37, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280065 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [60, 51, 60, 39, 17, 51, 51, 9, 3, 1, 3, 3, 1, 1, 1, 1, 11, 11, 11, 1, 1, 51, 51, 51, 51, 51, 51, 1, 11, 11, 11, 11, 11, 11, 11, 1, 51, 51] 119 rigid atoms, others: [35, 9, 12, 13, 14, 15, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280065 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280065 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280065/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280065 Building REAL300000280066 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280066' /scratch/stefan/7769901/working/building/REAL300000280066 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280066 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280066/0 /scratch/stefan/7769901/working/building/REAL300000280066 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/93 `/scratch/stefan/7769901/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCC2)C=C1) `REAL300000280066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280066 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 76, 76, 98, 98, 42, 17, 6, 17, 17, 6, 6, 6, 6, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 6, 6, 1, 1, 1, 1, 1, 1, 1, 98, 98] 98 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37]) total number of confs: 378 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280066 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 73, 73, 73, 73, 73, 98, 98, 98, 1, 1, 2, 2, 1, 1, 73, 73, 98, 98, 98, 98, 98, 98, 98, 1, 1] 98 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 37, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280066 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [78, 73, 78, 44, 44, 73, 73, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 73, 73, 73, 73, 73, 73, 1, 1, 6, 6, 6, 6, 6, 6, 6, 73, 73] 98 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 353 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280066 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280066 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280066/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280066 Building REAL300000280067 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280067' /scratch/stefan/7769901/working/building/REAL300000280067 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280067 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280067/0 /scratch/stefan/7769901/working/building/REAL300000280067 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/94 `/scratch/stefan/7769901/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CCC2)C=C1) `REAL300000280067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280067 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 120, 58, 17, 58, 58, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280067 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 92, 92, 92, 92, 92, 173, 201, 201, 201, 1, 1, 2, 2, 1, 1, 92, 92, 173, 173, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280067 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 112, 92, 92, 92, 92, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 92, 92, 92, 92, 92, 92, 1, 1, 6, 6, 17, 17, 17, 17, 17, 17, 17, 92, 92] 201 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280067 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280067 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280067/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280067 Building REAL300000280068 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280068' /scratch/stefan/7769901/working/building/REAL300000280068 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280068 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280068/0 /scratch/stefan/7769901/working/building/REAL300000280068 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/95 `/scratch/stefan/7769901/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12) `REAL300000280068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280068 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 4, 4, 4, 8, 20, 20, 12, 20, 36, 43, 43, 20, 20, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 20, 20, 36, 36, 20, 20, 1, 1, 1, 1] 72 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 39, 40, 22, 23, 24, 25, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280068 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 20, 62, 20, 20, 20, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 20, 20, 20, 20, 20, 20, 62, 62, 62, 20, 20, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20] 72 rigid atoms, others: [33, 34, 37, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280068 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280068/1 /scratch/stefan/7769901/working/building/REAL300000280068 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/96 `/scratch/stefan/7769901/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12) `REAL300000280068.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280068 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 15, 19, 33, 47, 47, 19, 19, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 7, 19, 19, 33, 33, 19, 19, 1, 1, 1, 1] 67 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 43, 40, 22, 23, 24, 25, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280068 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [51, 51, 19, 51, 19, 19, 19, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 19, 19, 19, 19, 19, 19, 51, 51, 51, 19, 19, 6, 1, 1, 3, 3, 1, 1, 19, 19, 19, 19] 67 rigid atoms, others: [34, 35, 38, 39, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280068 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280068 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280068/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280068/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280068 Building REAL300000280069 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280069' /scratch/stefan/7769901/working/building/REAL300000280069 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280069 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280069/0 /scratch/stefan/7769901/working/building/REAL300000280069 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/97 `/scratch/stefan/7769901/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280069 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 13, 13, 10, 13, 13, 19, 19, 13, 13, 19, 19, 19, 19, 19, 1, 1, 13, 13, 13, 1, 13, 13, 13, 13, 13, 13] 49 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 11, 12, 13, 37] set([0, 1, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280069 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 31, 13, 13, 13, 13, 13, 13, 35, 35, 35, 13, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 43, 43, 43, 43, 43, 13, 13, 35, 35, 35, 13, 1, 1, 3, 3, 1, 1] 49 rigid atoms, others: [38, 39, 42, 43, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280069 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280069/1 /scratch/stefan/7769901/working/building/REAL300000280069 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/98 `/scratch/stefan/7769901/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280069.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280069 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 13, 13, 10, 13, 13, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 12, 12, 12, 1, 7, 13, 13, 13, 13, 13, 13] 75 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 11, 12, 13, 37] set([0, 1, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280069 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [57, 25, 13, 13, 13, 13, 13, 13, 51, 51, 51, 13, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 57, 57, 57, 57, 57, 13, 13, 51, 51, 51, 13, 4, 1, 1, 3, 3, 1, 1] 75 rigid atoms, others: [39, 40, 43, 44, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280069 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280069 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280069/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280069/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280069 Building REAL300000280070 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280070' /scratch/stefan/7769901/working/building/REAL300000280070 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280070 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280070/0 /scratch/stefan/7769901/working/building/REAL300000280070 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/99 `/scratch/stefan/7769901/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(O)C=CC=C2OC(F)(F)F)C=C1) `REAL300000280070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280070 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 2, 2, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 1, 1, 10, 5, 5, 5, 1, 1] 10 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280070 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 5, 5] 10 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280070 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280070/1 /scratch/stefan/7769901/working/building/REAL300000280070 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/100 `/scratch/stefan/7769901/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C([O-])C=CC=C2OC(F)(F)F)C=C1) `REAL300000280070.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280070 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C([O-])C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 1, 1, 5, 5, 5, 1, 1] 5 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280070 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C([O-])C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 5 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280070 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280070 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280070/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280070/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280070 Building REAL300000280071 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280071' /scratch/stefan/7769901/working/building/REAL300000280071 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280071 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280071/0 /scratch/stefan/7769901/working/building/REAL300000280071 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/101 `/scratch/stefan/7769901/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)COC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=NN2C1) `REAL300000280071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280071 none CC1(C)COC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=NN2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 21, 28, 28, 25, 25, 33, 33, 33, 28, 28, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 28, 28, 33, 33, 28, 28, 1, 1, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 40, 41, 7, 21, 22, 23, 24, 39, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280071 none CC1(C)COC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=NN2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 28, 28, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 1, 1, 28, 28, 28] 33 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280071 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280071 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280071/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280071 Building REAL300000280072 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280072' /scratch/stefan/7769901/working/building/REAL300000280072 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280072 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280072/0 /scratch/stefan/7769901/working/building/REAL300000280072 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/102 `/scratch/stefan/7769901/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3=CC=CC=C3)S2)C=C1) `REAL300000280072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280072 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 63, 69, 69, 53, 18, 3, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 69, 69, 69, 69, 69, 69, 3, 1, 1, 1, 1, 1, 69, 69] 69 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 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, 35, 36]) total number of confs: 171 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280072 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 1, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26, 27, 28, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280072 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(C3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 43, 69, 69, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 69, 69, 69, 69, 69, 69, 1, 3, 3, 2, 3, 3, 69, 69] 69 rigid atoms, others: [9, 12, 13, 14, 15, 16, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280072 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280072 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280072/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280072 Building REAL300000280073 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280073' /scratch/stefan/7769901/working/building/REAL300000280073 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280073 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280073/0 /scratch/stefan/7769901/working/building/REAL300000280073 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/103 `/scratch/stefan/7769901/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)COC3=C2)C=C1) `REAL300000280073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280073 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)COC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 6, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280073 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)COC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 17, 17, 19, 19, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280073 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280073/1 /scratch/stefan/7769901/working/building/REAL300000280073 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/104 `/scratch/stefan/7769901/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)COC3=C2)C=C1) `REAL300000280073.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280073 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)COC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280073 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)COC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 17, 17, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280073 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280073 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280073/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280073/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280073 Building REAL300000280074 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280074' /scratch/stefan/7769901/working/building/REAL300000280074 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280074 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280074/0 /scratch/stefan/7769901/working/building/REAL300000280074 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/105 `/scratch/stefan/7769901/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=CO2)C=C1) `REAL300000280074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280074 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=CO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 103, 103, 103, 103, 103, 1, 1, 2, 2, 1, 1, 103, 103, 1, 1] 103 rigid atoms, others: [3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280074 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=CO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 79, 103, 103, 33, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 1, 1, 103, 103] 103 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280074 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280074 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280074/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280074 Building REAL300000280075 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280075' /scratch/stefan/7769901/working/building/REAL300000280075 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280075 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280075/0 /scratch/stefan/7769901/working/building/REAL300000280075 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/106 `/scratch/stefan/7769901/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280075 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 10, 10, 25, 31, 31, 13, 13, 1, 1, 1, 7, 7, 7, 1, 5, 13, 13, 25, 25, 13, 13, 1] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280075 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 13, 13, 13, 31, 31, 31, 13, 6, 1, 1, 2, 2, 1, 1, 13] 31 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280075 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280075/1 /scratch/stefan/7769901/working/building/REAL300000280075 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/107 `/scratch/stefan/7769901/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280075.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280075 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 14, 14, 14, 14, 23, 27, 27, 14, 14, 1, 1, 1, 7, 7, 7, 1, 14, 14, 23, 23, 14, 14, 1] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280075 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 14, 13, 14, 14, 14, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 14, 14, 14, 27, 27, 27, 14, 1, 1, 2, 2, 1, 1, 14] 27 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280075 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280075 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280075/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280075/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280075 Building REAL300000280076 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280076' /scratch/stefan/7769901/working/building/REAL300000280076 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280076 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280076/0 /scratch/stefan/7769901/working/building/REAL300000280076 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/108 `/scratch/stefan/7769901/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3CCCCN23)C=C1) `REAL300000280076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280076 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3CCCCN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 37, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280076 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3CCCCN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 16, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280076 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280076/1 /scratch/stefan/7769901/working/building/REAL300000280076 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/109 `/scratch/stefan/7769901/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C3CCCCN23)C=C1) `REAL300000280076.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280076 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C3CCCCN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 38, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280076 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C3CCCCN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 28, 28, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [32, 33, 34, 35, 36, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280076 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280076 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280076/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280076/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280076 Building REAL300000280077 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280077' /scratch/stefan/7769901/working/building/REAL300000280077 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280077 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280077/0 /scratch/stefan/7769901/working/building/REAL300000280077 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/110 `/scratch/stefan/7769901/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F) `REAL300000280077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280077 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 51, 51, 34, 34, 79, 79, 79, 51, 51, 1, 1, 1, 4, 4, 4, 1, 51, 51, 79, 79, 51, 51, 1] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280077 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [69, 37, 37, 51, 51, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 51, 69, 69, 69, 51, 1, 1, 2, 2, 1, 1, 51] 79 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280077 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280077 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280077/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280077 Building REAL300000280078 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280078' /scratch/stefan/7769901/working/building/REAL300000280078 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280078 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280078/0 /scratch/stefan/7769901/working/building/REAL300000280078 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/111 `/scratch/stefan/7769901/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300000280078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280078 none COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 17, 17, 11, 13, 33, 33, 33, 17, 17, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 5, 17, 17, 33, 33, 17, 17, 1, 2, 2, 2] 33 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 44, 23, 24, 25, 29] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280078 none COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [25, 17, 17, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 17, 17, 25, 25, 25, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17] 33 rigid atoms, others: [38, 39, 42, 43, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280078 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280078 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280078/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280078 Building REAL300000280079 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280079' /scratch/stefan/7769901/working/building/REAL300000280079 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280079 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280079/0 /scratch/stefan/7769901/working/building/REAL300000280079 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/112 `/scratch/stefan/7769901/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280079 none CC(C)OC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 52, 52, 36, 36, 90, 107, 107, 52, 52, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 52, 52, 90, 90, 52, 52] 155 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 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: 501 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280079 none CC(C)OC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [139, 114, 139, 52, 52, 52, 27, 52, 52, 52, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 139, 139, 139, 139, 139, 139, 139, 52, 27, 52, 1, 1, 2, 2, 1, 1] 155 rigid atoms, others: [35, 36, 39, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 424 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280079 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280079/1 /scratch/stefan/7769901/working/building/REAL300000280079 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/113 `/scratch/stefan/7769901/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280079.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280079 none CC(C)OC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [19, 8, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 62, 62, 47, 47, 108, 132, 132, 62, 62, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 25, 62, 62, 108, 108, 62, 62] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 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]) total number of confs: 617 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280079 none CC(C)OC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [176, 139, 176, 62, 62, 62, 31, 62, 62, 62, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 176, 176, 176, 176, 176, 176, 176, 62, 17, 62, 6, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [36, 37, 40, 41, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 563 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280079 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280079 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280079/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280079/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280079 Building REAL300000280080 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280080' /scratch/stefan/7769901/working/building/REAL300000280080 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280080 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280080/0 /scratch/stefan/7769901/working/building/REAL300000280080 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/114 `/scratch/stefan/7769901/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280080 none CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 14, 25, 25, 25, 25, 29, 29, 29, 25, 25, 2, 2, 2, 1, 2, 2, 2, 25, 25, 29, 29, 25, 25] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280080 none CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1] 29 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280080 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280080/1 /scratch/stefan/7769901/working/building/REAL300000280080 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/115 `/scratch/stefan/7769901/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280080.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280080 none CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 8, 8, 14, 17, 17, 17, 17, 27, 27, 27, 17, 17, 2, 2, 2, 1, 2, 2, 2, 14, 17, 17, 27, 27, 17, 17] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280080 none CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 17, 17, 17, 17, 17, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 2, 2, 1, 1] 27 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 69 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280080 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280080 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280080/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280080/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280080 Building REAL300000280081 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280081' /scratch/stefan/7769901/working/building/REAL300000280081 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280081 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280081/0 /scratch/stefan/7769901/working/building/REAL300000280081 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/116 `/scratch/stefan/7769901/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C2O1) `REAL300000280081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280081 none CC1CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 45, 45, 35, 45, 56, 56, 56, 45, 45, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 45, 45, 56, 56, 45, 45] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280081 none CC1CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 45, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 3, 3, 1, 1] 56 rigid atoms, others: [33, 34, 37, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280081 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280081/1 /scratch/stefan/7769901/working/building/REAL300000280081 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/117 `/scratch/stefan/7769901/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C2O1) `REAL300000280081.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280081 none CC1CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 43, 43, 38, 43, 53, 53, 53, 43, 43, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 23, 43, 43, 53, 53, 43, 43] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280081 none CC1CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 43, 43, 43, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 1, 1, 3, 3, 1, 1] 53 rigid atoms, others: [34, 35, 38, 39, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280081 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280081 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280081/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280081/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280081 Building REAL300000280082 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280082' /scratch/stefan/7769901/working/building/REAL300000280082 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280082 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280082/0 /scratch/stefan/7769901/working/building/REAL300000280082 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/118 `/scratch/stefan/7769901/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1) `REAL300000280082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280082 none CC(C)(C)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 22, 42, 42, 31, 31, 59, 63, 63, 42, 42, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 42, 42, 59, 59, 42, 42] 91 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 22] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280082 none CC(C)(C)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [75, 42, 75, 75, 42, 42, 42, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 42, 75, 75, 75, 75, 75, 75, 75, 75, 75, 42, 1, 1, 2, 2, 1, 1] 91 rigid atoms, others: [33, 34, 37, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280082 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280082 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280082/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280082 Building REAL300000280083 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280083' /scratch/stefan/7769901/working/building/REAL300000280083 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280083 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280083/0 /scratch/stefan/7769901/working/building/REAL300000280083 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/119 `/scratch/stefan/7769901/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1(C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1) `REAL300000280083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 18, 10, 18, 18, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 18, 18, 44, 44, 18, 18, 5, 1, 1, 2, 2, 1, 1, 18, 18, 44, 44, 44, 44] 52 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 193 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 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, 7, 7, 5, 6, 11, 11, 11, 29, 44, 44, 36, 37, 52, 52, 52, 44, 44, 7, 7, 1, 1, 7, 7, 29, 44, 44, 52, 52, 44, 44, 7, 7, 1, 1, 1, 1] 52 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 13, 14, 32, 42, 42, 18, 18, 1, 1, 7, 7, 1, 1, 9, 18, 18, 32, 32, 18, 18, 1, 1, 7, 7, 7, 7] 52 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 201 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280083 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280083/1 /scratch/stefan/7769901/working/building/REAL300000280083 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/120 `/scratch/stefan/7769901/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1) `REAL300000280083.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 20, 20, 20, 20, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 20, 20, 53, 53, 20, 20, 1, 1, 2, 2, 1, 1, 20, 20, 53, 53, 53, 53] 53 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 27, 53, 53, 38, 38, 53, 53, 53, 53, 53, 5, 5, 1, 1, 5, 5, 53, 53, 53, 53, 53, 53, 5, 5, 1, 1, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 35, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280083 none N#CC1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 13, 13, 37, 45, 45, 20, 20, 1, 1, 5, 5, 1, 1, 20, 20, 37, 37, 20, 20, 1, 1, 5, 5, 5, 5] 53 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 21, 22, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280083 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280083 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280083/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280083/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280083 Building REAL300000280084 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280084' /scratch/stefan/7769901/working/building/REAL300000280084 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280084 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280084/0 /scratch/stefan/7769901/working/building/REAL300000280084 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/121 `/scratch/stefan/7769901/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280084 none COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 69, 69, 43, 43, 108, 115, 115, 69, 69, 6, 6, 6, 1, 1, 69, 69, 108, 108, 69, 69] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280084 none COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [93, 69, 69, 69, 69, 69, 69, 69, 69, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 93, 93, 93, 69, 69, 1, 1, 2, 2, 1, 1] 115 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280084 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280084 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280084/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280084 Building REAL300000280085 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280085' /scratch/stefan/7769901/working/building/REAL300000280085 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280085 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280085/0 /scratch/stefan/7769901/working/building/REAL300000280085 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/122 `/scratch/stefan/7769901/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)C=CC3=C2OCCO3)C=C1) `REAL300000280085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280085 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)C=CC3=C2OCCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280085 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)C=CC3=C2OCCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 49, 53, 53, 19, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280085 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280085 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280085/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280085 Building REAL300000280086 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280086' /scratch/stefan/7769901/working/building/REAL300000280086 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280086 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280086/0 /scratch/stefan/7769901/working/building/REAL300000280086 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/123 `/scratch/stefan/7769901/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280086 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1] 20 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 45, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280086 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 20, 19, 19, 19, 19, 19, 19, 19, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 19, 19, 20, 20, 20, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 2, 2, 1, 1, 19] 20 rigid atoms, others: [39, 40, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 69 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280086 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280086/1 /scratch/stefan/7769901/working/building/REAL300000280086 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/124 `/scratch/stefan/7769901/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300000280086.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280086 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 23, 23, 35, 35, 35, 23, 23, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 35, 35, 23, 23, 1] 50 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 44, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 128 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280086 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 48, 23, 23, 23, 23, 23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 23, 23, 48, 48, 48, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 23] 50 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 159 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280086 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280086 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280086/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280086/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280086 Building REAL300000280087 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280087' /scratch/stefan/7769901/working/building/REAL300000280087 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280087 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280087/0 /scratch/stefan/7769901/working/building/REAL300000280087 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/125 `/scratch/stefan/7769901/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2Cl)C=C1) `REAL300000280087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280087 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 33, 33, 33, 33, 33, 1, 1, 2, 2, 1, 1, 33, 33, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280087 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 30, 33, 33, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 33, 33] 33 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280087 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280087 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280087/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280087 Building REAL300000280088 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280088' /scratch/stefan/7769901/working/building/REAL300000280088 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280088 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280088/0 /scratch/stefan/7769901/working/building/REAL300000280088 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/126 `/scratch/stefan/7769901/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(Br)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280088 none CN1N=C(Br)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 19, 31, 31, 26, 31, 43, 43, 43, 31, 31, 2, 2, 2, 1, 31, 31, 43, 43, 31, 31] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280088 none CN1N=C(Br)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [31, 31, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 31, 31, 31, 31, 1, 1, 2, 2, 1, 1] 43 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280088 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280088 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280088/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280088 Building REAL300000280089 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280089' /scratch/stefan/7769901/working/building/REAL300000280089 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280089 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280089/0 /scratch/stefan/7769901/working/building/REAL300000280089 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/127 `/scratch/stefan/7769901/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)(F)F)=C2)C=C1) `REAL300000280089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280089 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 23, 23, 23, 1, 1] 23 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280089 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 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, 23, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 23, 23] 23 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280089 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280089/1 /scratch/stefan/7769901/working/building/REAL300000280089 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/128 `/scratch/stefan/7769901/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)(F)F)=C2)C=C1) `REAL300000280089.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280089 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 1, 7, 22, 22, 22, 1, 1] 22 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280089 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 17, 22, 22, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 22, 22] 22 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280089 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280089 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280089/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280089/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280089 Building REAL300000280090 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280090' /scratch/stefan/7769901/working/building/REAL300000280090 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280090 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280090/0 /scratch/stefan/7769901/working/building/REAL300000280090 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/129 `/scratch/stefan/7769901/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280090 none CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 12, 12, 12, 30, 52, 52, 48, 48, 81, 81, 81, 52, 52, 2, 2, 2, 1, 1, 1, 52, 52, 81, 81, 52, 52] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280090 none CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 52, 52, 52, 52, 52, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 52, 52, 52, 52, 52, 52, 1, 1, 2, 2, 1, 1] 81 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280090 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280090 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280090/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280090 Building REAL300000280091 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280091' /scratch/stefan/7769901/working/building/REAL300000280091 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280091 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280091/0 /scratch/stefan/7769901/working/building/REAL300000280091 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/130 `/scratch/stefan/7769901/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=NON=C3C=C2)C=C1) `REAL300000280091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280091 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=NON=C3C=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 1, 1, 7, 20, 20, 20, 1, 1] 20 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280091 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=NON=C3C=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 9, 1, 1, 1, 20, 20] 20 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280091 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280091/1 /scratch/stefan/7769901/working/building/REAL300000280091 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/131 `/scratch/stefan/7769901/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=NON=C3C=C2)C=C1) `REAL300000280091.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280091 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=NON=C3C=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280091 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=NON=C3C=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 18, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280091 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280091 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280091/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280091/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280091 Building REAL300000280092 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280092' /scratch/stefan/7769901/working/building/REAL300000280092 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280092 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280092/0 /scratch/stefan/7769901/working/building/REAL300000280092 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/132 `/scratch/stefan/7769901/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3S2)C=C1) `REAL300000280092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280092 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 1, 1] 38 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280092 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280092 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280092 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280092/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280092 Building REAL300000280093 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280093' /scratch/stefan/7769901/working/building/REAL300000280093 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280093 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280093/0 /scratch/stefan/7769901/working/building/REAL300000280093 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/133 `/scratch/stefan/7769901/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=C(Cl)C=C23)C=C1) `REAL300000280093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280093 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 1, 1] 54 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280093 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3NC=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 54, 54, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 54, 54] 54 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280093 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280093 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280093/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280093 Building REAL300000280094 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280094' /scratch/stefan/7769901/working/building/REAL300000280094 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280094 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280094/0 /scratch/stefan/7769901/working/building/REAL300000280094 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/134 `/scratch/stefan/7769901/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2CC2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280094 none CN1N=C(C2CC2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 48, 48, 48, 48, 147, 147, 48, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 48, 48, 48, 147, 147, 147, 147, 147, 48, 1, 1, 3, 3, 1, 1] 177 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280094 none CN1N=C(C2CC2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 13, 13, 1, 1, 1, 6, 6, 6, 23, 48, 48, 28, 23, 78, 116, 116, 48, 48, 2, 2, 2, 13, 13, 13, 13, 13, 1, 48, 48, 78, 78, 48, 48] 177 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 31] set([5, 6, 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]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280094 none CN1N=C(C2CC2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 53, 53, 53, 107, 147, 147, 116, 107, 177, 177, 177, 147, 147, 13, 13, 13, 1, 1, 1, 1, 1, 13, 147, 147, 177, 177, 147, 147] 177 rigid atoms, others: [3, 4, 5, 6, 26, 27, 28, 29, 30] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280094 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280094 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280094/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280094 Building REAL300000280095 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280095' /scratch/stefan/7769901/working/building/REAL300000280095 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280095 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280095/0 /scratch/stefan/7769901/working/building/REAL300000280095 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/135 `/scratch/stefan/7769901/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1F) `REAL300000280095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280095 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 15, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 9, 9, 8, 8, 13, 13, 13, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 9, 9, 13, 13, 9, 9, 2, 2, 2] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280095 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 1, 15, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 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, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 2, 2, 1, 1, 9, 9, 9] 13 rigid atoms, others: [32, 33, 36, 37, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40]) total number of confs: 42 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280095 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280095 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280095/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280095 Building REAL300000280096 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280096' /scratch/stefan/7769901/working/building/REAL300000280096 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280096 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280096/0 /scratch/stefan/7769901/working/building/REAL300000280096 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/136 `/scratch/stefan/7769901/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC) `REAL300000280096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280096 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 56, 56, 38, 38, 89, 101, 101, 56, 56, 1, 1, 4, 4, 4, 4, 1, 1, 1, 56, 56, 89, 89, 56, 56, 4, 4, 4] 118 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280096 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 56, 56, 56, 56, 56, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 56, 56, 90, 104, 104, 104, 56, 56, 56, 1, 1, 2, 2, 1, 1, 90, 90, 90] 118 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280096 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280096/1 /scratch/stefan/7769901/working/building/REAL300000280096 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/137 `/scratch/stefan/7769901/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1OC) `REAL300000280096.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280096 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 38, 37, 80, 86, 86, 49, 49, 1, 1, 4, 4, 4, 4, 1, 1, 1, 25, 49, 49, 80, 80, 49, 49, 5, 5, 5] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280096 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [82, 49, 49, 49, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 49, 49, 77, 82, 82, 82, 49, 49, 49, 6, 1, 1, 2, 2, 1, 1, 77, 77, 77] 98 rigid atoms, others: [32, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280096 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280096 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280096/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280096/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280096 Building REAL300000280097 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280097' /scratch/stefan/7769901/working/building/REAL300000280097 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280097 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280097/0 /scratch/stefan/7769901/working/building/REAL300000280097 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/138 `/scratch/stefan/7769901/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3OCCNC(=O)C3=C2)C=C1) `REAL300000280097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280097 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3OCCNC(=O)C3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280097 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3OCCNC(=O)C3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 14 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 40, 39, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280097 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280097/1 /scratch/stefan/7769901/working/building/REAL300000280097 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/139 `/scratch/stefan/7769901/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCNC(=O)C3=C2)C=C1) `REAL300000280097.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280097 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCNC(=O)C3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 24, 25, 38, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280097 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCNC(=O)C3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280097 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280097 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280097/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280097/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280097 Building REAL300000280098 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280098' /scratch/stefan/7769901/working/building/REAL300000280098 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280098 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280098/0 /scratch/stefan/7769901/working/building/REAL300000280098 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/140 `/scratch/stefan/7769901/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br) `REAL300000280098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280098 none N#CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 15, 15, 20, 20, 20, 18, 18, 1, 1, 1, 1, 1, 9, 18, 18, 20, 20, 18, 18, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280098 none N#CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 18, 18, 18, 18, 18, 6, 1, 1, 2, 2, 1, 1, 18, 18] 20 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280098 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280098/1 /scratch/stefan/7769901/working/building/REAL300000280098 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/141 `/scratch/stefan/7769901/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br) `REAL300000280098.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280098 none N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 15, 15, 23, 23, 23, 20, 20, 1, 1, 1, 1, 1, 20, 20, 23, 23, 20, 20, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280098 none N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 1, 1, 20, 20] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 26, 27, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280098 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280098 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280098/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280098/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280098 Building REAL300000280099 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280099' /scratch/stefan/7769901/working/building/REAL300000280099 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280099 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280099/0 /scratch/stefan/7769901/working/building/REAL300000280099 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/142 `/scratch/stefan/7769901/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=COC3=CC=CC=C23)C=C1) `REAL300000280099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280099 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=COC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280099 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=COC3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 45, 45, 53, 53, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280099 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280099 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280099/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280099 Building REAL300000280100 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280100' /scratch/stefan/7769901/working/building/REAL300000280100 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280100 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280100/0 /scratch/stefan/7769901/working/building/REAL300000280100 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/143 `/scratch/stefan/7769901/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC) `REAL300000280100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280100 none COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 78, 78, 49, 49, 128, 136, 136, 78, 78, 1, 1, 4, 4, 4, 4, 1, 1, 78, 78, 128, 128, 78, 78, 4, 4, 4] 185 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280100 none COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [137, 78, 78, 78, 78, 78, 78, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 78, 78, 123, 137, 137, 137, 78, 78, 1, 1, 2, 2, 1, 1, 123, 123, 123] 185 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280100 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280100 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280100/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280100 Building REAL300000280101 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280101' /scratch/stefan/7769901/working/building/REAL300000280101 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280101 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280101/0 /scratch/stefan/7769901/working/building/REAL300000280101 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/144 `/scratch/stefan/7769901/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCCC2)=N1) `REAL300000280101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280101 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 22, 22, 22, 50, 97, 97, 97, 97, 109, 109, 109, 97, 97, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 97, 97, 109, 109, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 1] 109 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280101 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 7, 7, 7, 23, 62, 62, 62, 62, 91, 95, 95, 62, 62, 1, 1, 6, 6, 6, 6, 1, 2, 2, 2, 1, 62, 62, 91, 91, 62, 62, 6, 6, 6, 6, 6, 6, 6, 6, 6] 109 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280101 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 62, 62, 97, 97, 97, 97, 62, 62, 62, 62, 62, 1, 1, 2, 2, 1, 1, 97, 97, 97, 97, 97, 97, 97, 97, 97] 109 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280101 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280101 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280101/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280101 Building REAL300000280102 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280102' /scratch/stefan/7769901/working/building/REAL300000280102 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280102 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280102/0 /scratch/stefan/7769901/working/building/REAL300000280102 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/145 `/scratch/stefan/7769901/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1) `REAL300000280102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280102 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 26, 26, 26, 56, 82, 82, 70, 82, 109, 109, 109, 82, 82, 1, 1, 1, 1, 6, 7, 7, 7, 6, 82, 82, 109, 109, 82, 82, 1, 1, 1, 1, 1] 109 rigid atoms, others: [33, 34, 35, 36, 37, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280102 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 23, 43, 43, 33, 43, 69, 74, 74, 43, 43, 1, 1, 6, 6, 1, 2, 2, 2, 1, 43, 43, 69, 69, 43, 43, 6, 6, 6, 6, 6] 109 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280102 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 43, 43, 82, 82, 43, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1, 82, 82, 82, 82, 82] 109 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280102 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280102 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280102/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280102 Building REAL300000280103 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280103' /scratch/stefan/7769901/working/building/REAL300000280103 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280103 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280103/0 /scratch/stefan/7769901/working/building/REAL300000280103 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/146 `/scratch/stefan/7769901/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)F)C=C2)C=C1) `REAL300000280103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280103 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 127, 143, 143, 20, 20, 1, 1, 2, 2, 1, 1, 9, 20, 20, 143, 20, 20, 1, 1] 143 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280103 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 20, 46, 16, 9, 20, 20, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 12, 39, 39, 1, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 39, 1, 1, 20, 20] 143 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280103 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280103 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280103/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280103 Building REAL300000280104 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280104' /scratch/stefan/7769901/working/building/REAL300000280104 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280104 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280104/0 /scratch/stefan/7769901/working/building/REAL300000280104 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/147 `/scratch/stefan/7769901/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=C2OCO3)C=C1) `REAL300000280104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280104 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 22, 23, 24, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280104 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 28, 37, 57, 57, 28, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280104 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280104 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280104/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280104 Building REAL300000280105 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280105' /scratch/stefan/7769901/working/building/REAL300000280105 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280105 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280105/0 /scratch/stefan/7769901/working/building/REAL300000280105 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/148 `/scratch/stefan/7769901/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=CC=C21) `REAL300000280105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280105 none CN1N=NC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 19, 37, 37, 27, 27, 37, 37, 37, 37, 37, 1, 1, 1, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 1, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 35, 20, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280105 none CN1N=NC2=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 1, 1, 37, 37, 37] 37 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280105 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280105 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280105/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280105 Building REAL300000280106 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280106' /scratch/stefan/7769901/working/building/REAL300000280106 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280106 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280106/0 /scratch/stefan/7769901/working/building/REAL300000280106 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/149 `/scratch/stefan/7769901/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1Br) `REAL300000280106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280106 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 5, 15, 15, 15, 13, 13, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 13, 13, 15, 15, 13, 13, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280106 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 3, 3, 1, 1, 13] 15 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280106 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280106 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280106/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280106 Building REAL300000280107 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280107' /scratch/stefan/7769901/working/building/REAL300000280107 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280107 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280107/0 /scratch/stefan/7769901/working/building/REAL300000280107 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/150 `/scratch/stefan/7769901/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C21) `REAL300000280107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280107 none CN1C=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 5, 13, 13, 13, 13, 16, 16, 16, 13, 13, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 13, 16, 16, 13, 13] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280107 none CN1C=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 1] 16 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280107 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280107/1 /scratch/stefan/7769901/working/building/REAL300000280107 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/151 `/scratch/stefan/7769901/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C21) `REAL300000280107.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280107 none CN1C=CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 7, 13, 13, 13, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 7, 7, 13, 13, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280107 none CN1C=CC2=CC=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 1, 2, 2, 1, 1] 13 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 31 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280107 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280107 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280107/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280107/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280107 Building REAL300000280108 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280108' /scratch/stefan/7769901/working/building/REAL300000280108 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280108 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280108/0 /scratch/stefan/7769901/working/building/REAL300000280108 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/152 `/scratch/stefan/7769901/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1N) `REAL300000280108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280108 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 13, 12, 21, 21, 21, 15, 15, 1, 1, 1, 1, 2, 2, 2, 1, 9, 15, 15, 21, 21, 15, 15, 1, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280108 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 4, 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, 15, 15, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 2, 2, 1, 1, 15, 15, 15] 21 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280108 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280108/1 /scratch/stefan/7769901/working/building/REAL300000280108 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/153 `/scratch/stefan/7769901/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1N) `REAL300000280108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280108 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 4, 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, 3, 3, 3, 9, 23, 23, 14, 14, 25, 25, 25, 23, 23, 1, 1, 1, 1, 2, 2, 2, 1, 23, 23, 25, 25, 23, 23, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280108 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 23, 23, 23] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280108 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280108 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280108/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280108/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280108 Building REAL300000280109 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280109' /scratch/stefan/7769901/working/building/REAL300000280109 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280109 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280109/0 /scratch/stefan/7769901/working/building/REAL300000280109 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/154 `/scratch/stefan/7769901/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280109 none COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 52, 52, 52, 52, 73, 74, 74, 52, 52, 4, 4, 4, 1, 52, 52, 73, 73, 52, 52] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280109 none COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [73, 52, 52, 52, 52, 52, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 73, 73, 73, 52, 1, 1, 2, 2, 1, 1] 76 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 27, 28]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280109 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280109 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280109/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280109 Building REAL300000280110 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280110' /scratch/stefan/7769901/working/building/REAL300000280110 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280110 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280110/0 /scratch/stefan/7769901/working/building/REAL300000280110 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/155 `/scratch/stefan/7769901/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1) `REAL300000280110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280110 none CC1(C)CCCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 39, 39, 17, 17, 44, 44, 44, 39, 39, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 17, 39, 39, 44, 44, 39, 39, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 41, 42, 7, 21, 33, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280110 none CC1(C)CCCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [39, 39, 39, 39, 39, 39, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 1, 1, 3, 3, 1, 1, 39, 39] 44 rigid atoms, others: [35, 36, 39, 40, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280110 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280110 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280110/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280110 Building REAL300000280111 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280111' /scratch/stefan/7769901/working/building/REAL300000280111 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280111 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280111/0 /scratch/stefan/7769901/working/building/REAL300000280111 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/156 `/scratch/stefan/7769901/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(F)=CC(Cl)=C3OC2)C=C1) `REAL300000280111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280111 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(F)=CC(Cl)=C3OC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 13, 119, 119, 119, 119, 119, 1, 1] 119 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 37, 24, 25, 26, 27, 28, 29, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280111 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(F)=CC(Cl)=C3OC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 44, 62, 119, 119, 44, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 44, 1, 1, 1, 1, 1, 119, 119] 119 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 37, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280111 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280111 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280111/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280111 Building REAL300000280112 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280112' /scratch/stefan/7769901/working/building/REAL300000280112 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280112 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280112/0 /scratch/stefan/7769901/working/building/REAL300000280112 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/157 `/scratch/stefan/7769901/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=C3C=COC3=C(F)C=C2)C=C1) `REAL300000280112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280112 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=C3C=COC3=C(F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 2, 2, 1, 1, 11, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280112 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=C3C=COC3=C(F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 23, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 33, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280112 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280112/1 /scratch/stefan/7769901/working/building/REAL300000280112 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/158 `/scratch/stefan/7769901/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3C=COC3=C(F)C=C2)C=C1) `REAL300000280112.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280112 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3C=COC3=C(F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 2, 2, 1, 1, 46, 46, 46, 46, 1, 1] 46 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280112 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3C=COC3=C(F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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: [46, 46, 46, 46, 46, 46, 46, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 46, 46] 46 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280112 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280112 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280112/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280112/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280112 Building REAL300000280113 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280113' /scratch/stefan/7769901/working/building/REAL300000280113 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280113 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280113/0 /scratch/stefan/7769901/working/building/REAL300000280113 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/159 `/scratch/stefan/7769901/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCC2)=N1) `REAL300000280113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280113 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 19, 19, 19, 45, 78, 78, 48, 45, 103, 103, 103, 78, 78, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 78, 78, 103, 103, 78, 78, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280113 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 23, 50, 50, 25, 23, 74, 79, 79, 50, 50, 1, 1, 6, 6, 6, 1, 2, 2, 2, 1, 50, 50, 74, 74, 50, 50, 6, 6, 6, 6, 6, 6, 6] 103 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280113 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 50, 50, 78, 78, 78, 50, 50, 50, 50, 50, 1, 1, 3, 3, 1, 1, 78, 78, 78, 78, 78, 78, 78] 103 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280113 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280113 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280113/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280113 Building REAL300000280114 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280114' /scratch/stefan/7769901/working/building/REAL300000280114 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280114 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280114/0 /scratch/stefan/7769901/working/building/REAL300000280114 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/160 `/scratch/stefan/7769901/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280114 none CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 13, 13, 10, 10, 21, 22, 22, 13, 13, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 21, 21, 13, 13, 1] 33 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 10, 7, 11, 49, 25] set([0, 2, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280114 none CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [22, 13, 22, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 13, 22, 22, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 2, 2, 1, 1, 13] 33 rigid atoms, others: [48, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 49]) total number of confs: 114 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280114 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280114/1 /scratch/stefan/7769901/working/building/REAL300000280114 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/161 `/scratch/stefan/7769901/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280114.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280114 none CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 8, 8, 21, 23, 23, 13, 13, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 21, 21, 13, 13, 1] 29 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 11, 35, 48, 25] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280114 none CC(C)C1=CC=C(C(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 13, 19, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 13, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 1, 13] 29 rigid atoms, others: [42, 43, 14, 15, 16, 17, 18, 19, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280114 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280114 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280114/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280114/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280114 Building REAL300000280115 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280115' /scratch/stefan/7769901/working/building/REAL300000280115 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280115 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280115/0 /scratch/stefan/7769901/working/building/REAL300000280115 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/162 `/scratch/stefan/7769901/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)SC=C2)C=C1) `REAL300000280115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280115 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)SC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 35, 35, 35, 35, 35, 1, 1, 2, 2, 1, 1, 35, 35, 1, 1] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280115 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)SC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 30, 35, 35, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 35, 35] 35 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280115 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280115 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280115/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280115 Building REAL300000280116 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280116' /scratch/stefan/7769901/working/building/REAL300000280116 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280116 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280116/0 /scratch/stefan/7769901/working/building/REAL300000280116 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/163 `/scratch/stefan/7769901/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CC3CCC3)N=C2)C=C1) `REAL300000280116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280116 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CC3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 182, 182, 201, 201, 121, 42, 23, 42, 42, 23, 23, 5, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 201, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 23, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280116 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CC3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 35, 35, 35, 141, 201, 201, 201, 35, 35, 1, 1, 2, 2, 1, 1, 35, 141, 141, 201, 201, 201, 201, 201, 201, 201, 35, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280116 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CC3CCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 35, 55, 15, 15, 35, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 9, 23, 23, 23, 1, 1, 35, 35, 35, 35, 35, 35, 1, 9, 9, 23, 23, 23, 23, 23, 23, 23, 1, 35, 35] 201 rigid atoms, others: [38, 9, 12, 13, 14, 15, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280116 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280116 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280116/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280116 Building REAL300000280117 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280117' /scratch/stefan/7769901/working/building/REAL300000280117 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280117 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280117/0 /scratch/stefan/7769901/working/building/REAL300000280117 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/164 `/scratch/stefan/7769901/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C3CC3)C=CS2)C=C1) `REAL300000280117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280117 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C3CC3)C=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [168, 168, 168, 168, 130, 168, 168, 73, 32, 7, 32, 32, 7, 1, 1, 1, 1, 7, 7, 7, 168, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 7, 7, 168, 168] 168 rigid atoms, others: [13, 14, 15, 16, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 486 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280117 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C3CC3)C=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 118, 118, 168, 168, 118, 118, 118, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 118, 118, 1, 1] 168 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280117 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C3CC3)C=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [123, 118, 123, 118, 65, 118, 118, 35, 11, 1, 11, 11, 1, 1, 1, 7, 7, 1, 1, 1, 118, 118, 118, 118, 118, 118, 7, 7, 7, 7, 7, 1, 1, 118, 118] 168 rigid atoms, others: [32, 9, 12, 13, 14, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280117 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280117 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280117/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280117 Building REAL300000280118 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280118' /scratch/stefan/7769901/working/building/REAL300000280118 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280118 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280118/0 /scratch/stefan/7769901/working/building/REAL300000280118 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/165 `/scratch/stefan/7769901/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1) `REAL300000280118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 197, 198, 201, 201, 155, 139, 87, 139, 139, 87, 87, 62, 66, 87, 87, 49, 10, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 87, 87, 87, 10, 10, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 53, 53, 53, 53, 53, 53, 53, 112, 167, 201, 201, 1, 1, 2, 2, 1, 1, 53, 53, 53, 167, 167, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 53, 72, 28, 28, 53, 53, 18, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 87, 87, 53, 53, 53, 53, 53, 53, 1, 1, 1, 33, 33, 87, 87, 87, 87, 87, 53, 53] 201 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280118 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280118/1 /scratch/stefan/7769901/working/building/REAL300000280118 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/166 `/scratch/stefan/7769901/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1) `REAL300000280118.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 200, 201, 201, 167, 149, 88, 149, 149, 88, 88, 70, 70, 88, 88, 54, 10, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 167, 88, 88, 88, 10, 10, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 637 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 41, 41, 41, 21, 41, 41, 41, 109, 168, 201, 201, 1, 1, 2, 2, 1, 1, 7, 41, 21, 41, 168, 168, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 683 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280118 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=CC=C2OCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 72, 24, 24, 41, 41, 16, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 88, 88, 41, 41, 41, 41, 41, 41, 16, 1, 1, 1, 31, 31, 88, 88, 88, 88, 88, 41, 41] 201 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280118 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280118 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280118/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280118/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280118 Building REAL300000280119 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280119' /scratch/stefan/7769901/working/building/REAL300000280119 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280119 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280119/0 /scratch/stefan/7769901/working/building/REAL300000280119 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/167 `/scratch/stefan/7769901/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280119 none CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 15, 35, 50, 50, 19, 19, 1, 1, 7, 7, 7, 7, 7, 7, 21, 21, 1, 1, 9, 19, 19, 35, 35, 19, 19, 1, 1] 126 rigid atoms, others: [1, 34, 35, 6, 7, 8, 9, 10, 43, 44, 24, 25] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280119 none CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [76, 19, 76, 76, 114, 114, 19, 19, 19, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 19, 76, 76, 76, 76, 76, 76, 114, 114, 19, 19, 6, 1, 1, 2, 2, 1, 1, 19, 19] 126 rigid atoms, others: [37, 38, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43, 44]) total number of confs: 436 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280119 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280119/1 /scratch/stefan/7769901/working/building/REAL300000280119 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/168 `/scratch/stefan/7769901/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280119.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280119 none CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 14, 14, 35, 44, 44, 19, 19, 1, 1, 7, 7, 7, 7, 7, 7, 20, 20, 1, 1, 19, 19, 35, 35, 19, 19, 1, 1] 105 rigid atoms, others: [1, 34, 35, 6, 7, 8, 9, 10, 43, 24, 25, 42] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280119 none CC(C)(C(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [81, 19, 81, 81, 101, 101, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 19, 81, 81, 81, 81, 81, 81, 101, 101, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19] 105 rigid atoms, others: [36, 37, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280119 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280119 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280119/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280119/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280119 Building REAL300000280120 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280120' /scratch/stefan/7769901/working/building/REAL300000280120 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280120 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280120/0 /scratch/stefan/7769901/working/building/REAL300000280120 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/169 `/scratch/stefan/7769901/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C2C=C1) `REAL300000280120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280120 none COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 11, 11, 11, 26, 63, 63, 43, 43, 97, 99, 99, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 63, 63, 97, 97, 63, 63, 1, 1, 1, 1, 1] 99 rigid atoms, others: [1, 2, 3, 4, 37, 35, 39, 18, 19, 20, 21, 22, 23, 24, 25, 38, 36] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280120 none COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [78, 63, 63, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 78, 78, 78, 1, 1, 2, 2, 1, 1, 63, 63, 63, 63, 63] 99 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280120 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280120 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280120/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280120 Building REAL300000280121 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280121' /scratch/stefan/7769901/working/building/REAL300000280121 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280121 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280121/0 /scratch/stefan/7769901/working/building/REAL300000280121 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/170 `/scratch/stefan/7769901/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280121 none CCCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 15, 15, 38, 65, 65, 22, 22, 1, 15, 15, 15, 14, 14, 6, 6, 1, 1, 1, 9, 22, 22, 38, 38, 22, 22, 1] 131 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 40, 22, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280121 none CCCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [102, 63, 22, 22, 22, 22, 22, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 22, 114, 114, 114, 114, 114, 63, 63, 22, 22, 22, 6, 1, 1, 2, 2, 1, 1, 22] 131 rigid atoms, others: [34, 35, 38, 39, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280121 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280121/1 /scratch/stefan/7769901/working/building/REAL300000280121 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/171 `/scratch/stefan/7769901/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280121.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280121 none CCCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 26, 26, 9, 9, 43, 67, 67, 26, 26, 1, 16, 16, 16, 15, 15, 7, 7, 1, 1, 1, 26, 26, 43, 43, 26, 26, 1] 137 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 39, 22, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280121 none CCCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [123, 76, 26, 26, 26, 26, 26, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 26, 131, 131, 131, 131, 131, 76, 76, 26, 26, 26, 1, 1, 3, 3, 1, 1, 26] 137 rigid atoms, others: [33, 34, 37, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280121 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280121 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280121/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280121/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280121 Building REAL300000280122 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280122' /scratch/stefan/7769901/working/building/REAL300000280122 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280122 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280122/0 /scratch/stefan/7769901/working/building/REAL300000280122 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/172 `/scratch/stefan/7769901/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280122 none COC(=O)C1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 37, 37, 23, 37, 57, 63, 63, 37, 37, 1, 13, 13, 13, 2, 2, 2, 37, 37, 57, 57, 37, 37, 1] 107 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 36] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280122 none COC(=O)C1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 85, 37, 85, 37, 37, 37, 37, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 37, 85, 85, 85, 37, 37, 37, 1, 1, 2, 2, 1, 1, 37] 107 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280122 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280122 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280122/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280122 Building REAL300000280123 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280123' /scratch/stefan/7769901/working/building/REAL300000280123 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280123 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280123/0 /scratch/stefan/7769901/working/building/REAL300000280123 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/173 `/scratch/stefan/7769901/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280123 none CN1N=C2CCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 46, 46, 30, 29, 72, 72, 72, 46, 46, 2, 2, 2, 1, 1, 1, 1, 1, 1, 46, 46, 72, 72, 46, 46] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280123 none CN1N=C2CCCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 46, 46, 46, 46, 46, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 3, 4, 4, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 3, 3, 1, 1] 72 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 117 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280123 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280123/1 /scratch/stefan/7769901/working/building/REAL300000280123 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/174 `/scratch/stefan/7769901/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280123.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280123 none CN1N=C2CCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 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, 1, 1, 1, 1, 12, 12, 12, 27, 42, 42, 40, 42, 67, 67, 67, 42, 42, 2, 2, 2, 1, 1, 1, 1, 1, 1, 27, 42, 42, 67, 67, 42, 42] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 275 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280123 none CN1N=C2CCCC2=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 2, 2, 1, 1] 67 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 116 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280123 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280123 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280123/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280123/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280123 Building REAL300000280124 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280124' /scratch/stefan/7769901/working/building/REAL300000280124 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280124 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280124/0 /scratch/stefan/7769901/working/building/REAL300000280124 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/175 `/scratch/stefan/7769901/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280124 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 1, 1, 11, 11, 11, 1, 1] 11 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280124 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11] 11 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280124 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280124/1 /scratch/stefan/7769901/working/building/REAL300000280124 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/176 `/scratch/stefan/7769901/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280124.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280124 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 1, 1] 11 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280124 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC([N+](=O)[O-])=CC([N+](=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 11, 11] 11 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280124 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280124 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280124/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280124/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280124 Building REAL300000280125 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280125' /scratch/stefan/7769901/working/building/REAL300000280125 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280125 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280125/0 /scratch/stefan/7769901/working/building/REAL300000280125 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/177 `/scratch/stefan/7769901/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1) `REAL300000280125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280125 none COC(=O)C1=CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 14, 35, 51, 51, 19, 19, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 9, 19, 19, 35, 35, 19, 19, 1, 1, 1] 73 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 41, 24, 25, 26, 27, 42, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280125 none COC(=O)C1=CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 19, 61, 19, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 19, 19, 19, 61, 61, 61, 19, 19, 19, 4, 1, 1, 2, 2, 1, 1, 19, 19, 19] 73 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280125 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280125/1 /scratch/stefan/7769901/working/building/REAL300000280125 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/178 `/scratch/stefan/7769901/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1) `REAL300000280125.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280125 none COC(=O)C1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 14, 14, 39, 59, 59, 23, 23, 1, 1, 1, 1, 13, 13, 13, 1, 1, 1, 23, 23, 39, 39, 23, 23, 1, 1, 1] 80 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 40, 41, 24, 25, 26, 27, 42, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280125 none COC(=O)C1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 23, 80, 23, 23, 23, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 23, 23, 23, 23, 80, 80, 80, 23, 23, 23, 1, 1, 2, 2, 1, 1, 23, 23, 23] 80 rigid atoms, others: [34, 35, 38, 39, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280125 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280125 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280125/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280125/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280125 Building REAL300000280126 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280126' /scratch/stefan/7769901/working/building/REAL300000280126 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280126 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280126/0 /scratch/stefan/7769901/working/building/REAL300000280126 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/179 `/scratch/stefan/7769901/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280126 none CC1=CC=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 7, 12, 12, 12, 7, 7, 2, 2, 2, 1, 1, 1, 2, 2, 2, 5, 7, 7, 12, 12, 7, 7] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280126 none CC1=CC=CC(C)=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 2, 2, 1, 1] 5 rigid atoms, others: [32, 33, 36, 37, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280126 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280126 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280126/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280126 Building REAL300000280127 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280127' /scratch/stefan/7769901/working/building/REAL300000280127 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280127 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280127/0 /scratch/stefan/7769901/working/building/REAL300000280127 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/180 `/scratch/stefan/7769901/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280127 none CC(C)(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 13, 13, 17, 17, 17, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 13, 13, 17, 17, 13, 13] 17 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 33] set([0, 2, 3, 10, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280127 none CC(C)(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 1, 1] 17 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280127 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280127 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280127/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280127 Building REAL300000280128 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280128' /scratch/stefan/7769901/working/building/REAL300000280128 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280128 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280128/0 /scratch/stefan/7769901/working/building/REAL300000280128 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/181 `/scratch/stefan/7769901/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280128 none CC(C)(C)N1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 13, 17, 29, 29, 29, 19, 19, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 19, 19, 29, 29, 19, 19, 1] 47 rigid atoms, others: [32, 1, 4, 5, 6, 7, 39, 21, 22] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280128 none CC(C)(C)N1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 43, 43, 19, 19, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 1, 1, 3, 3, 1, 1, 19] 47 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280128 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280128 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280128/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280128 Building REAL300000280129 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280129' /scratch/stefan/7769901/working/building/REAL300000280129 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280129 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280129/0 /scratch/stefan/7769901/working/building/REAL300000280129 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/182 `/scratch/stefan/7769901/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNN=C2C2CCC2)C=C1) `REAL300000280129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280129 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNN=C2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 92, 86, 106, 106, 46, 21, 7, 21, 21, 7, 7, 7, 7, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 7, 7, 1, 1, 1, 1, 1, 1, 1, 106, 106] 106 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280129 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNN=C2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 76, 76, 76, 76, 76, 106, 106, 106, 1, 1, 2, 2, 1, 1, 76, 76, 106, 106, 106, 106, 106, 106, 106, 1, 1] 106 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 37, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280129 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNN=C2C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [83, 76, 83, 46, 43, 76, 76, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 76, 76, 76, 76, 76, 76, 1, 1, 7, 7, 7, 7, 7, 7, 7, 76, 76] 106 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280129 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280129 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280129/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280129 Building REAL300000280130 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280130' /scratch/stefan/7769901/working/building/REAL300000280130 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280130 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280130/0 /scratch/stefan/7769901/working/building/REAL300000280130 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/183 `/scratch/stefan/7769901/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F) `REAL300000280130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280130 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 9, 9, 25, 25, 25, 23, 23, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 23, 23, 25, 25, 23, 23, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280130 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 3, 3, 1, 1, 23] 25 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280130 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280130/1 /scratch/stefan/7769901/working/building/REAL300000280130 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/184 `/scratch/stefan/7769901/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F) `REAL300000280130.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280130 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 14, 21, 21, 21, 19, 19, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 19, 19, 21, 21, 19, 19, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280130 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 2, 2, 1, 1, 19] 21 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280130 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280130 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280130/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280130/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280130 Building REAL300000280131 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280131' /scratch/stefan/7769901/working/building/REAL300000280131 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280131 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280131/0 /scratch/stefan/7769901/working/building/REAL300000280131 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/185 `/scratch/stefan/7769901/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280131 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 23, 23, 29, 29, 29, 23, 23, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 23, 23, 29, 29, 23, 23, 1] 41 rigid atoms, others: [1, 34, 4, 5, 6, 33, 8, 41, 7, 22, 23] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280131 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 23, 37, 37, 23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 23, 1, 1, 2, 2, 1, 1, 23] 41 rigid atoms, others: [35, 36, 39, 40, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280131 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280131/1 /scratch/stefan/7769901/working/building/REAL300000280131 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/186 `/scratch/stefan/7769901/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280131.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280131 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 18, 18, 22, 24, 24, 18, 18, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 9, 18, 18, 22, 22, 18, 18, 1] 35 rigid atoms, others: [1, 34, 4, 5, 6, 33, 8, 42, 7, 22, 23] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280131 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 30, 30, 18, 18, 18, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 6, 1, 1, 2, 2, 1, 1, 18] 35 rigid atoms, others: [36, 37, 40, 41, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280131 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280131 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280131/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280131/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280131 Building REAL300000280132 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280132' /scratch/stefan/7769901/working/building/REAL300000280132 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280132 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280132/0 /scratch/stefan/7769901/working/building/REAL300000280132 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/187 `/scratch/stefan/7769901/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=C2)C=C1) `REAL300000280132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280132 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21, 1, 1] 21 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280132 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 17, 17, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1, 1, 21, 21] 21 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 20, 21, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280132 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280132/1 /scratch/stefan/7769901/working/building/REAL300000280132 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/188 `/scratch/stefan/7769901/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=C2)C=C1) `REAL300000280132.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280132 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 6, 23, 23, 1, 1] 23 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280132 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C([N+](=O)[O-])=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 23, 9, 1, 1, 23, 23] 23 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280132 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280132 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280132/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280132/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280132 Building REAL300000280133 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280133' /scratch/stefan/7769901/working/building/REAL300000280133 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280133 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280133/0 /scratch/stefan/7769901/working/building/REAL300000280133 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/189 `/scratch/stefan/7769901/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=C2)C=C1) `REAL300000280133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280133 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 7, 21, 21, 21, 1, 1] 21 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280133 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280133 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280133/1 /scratch/stefan/7769901/working/building/REAL300000280133 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/190 `/scratch/stefan/7769901/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=C2)C=C1) `REAL300000280133.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280133 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21, 21, 1, 1] 21 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280133 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 21, 21] 21 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280133 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280133 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280133/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280133/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280133 Building REAL300000280134 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280134' /scratch/stefan/7769901/working/building/REAL300000280134 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280134 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280134/0 /scratch/stefan/7769901/working/building/REAL300000280134 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/191 `/scratch/stefan/7769901/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(CF)C=C2)C=C1) `REAL300000280134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280134 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(CF)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 27, 27, 27, 40, 27, 27, 1, 1, 2, 2, 1, 1, 11, 27, 27, 40, 40, 27, 27, 1, 1] 40 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280134 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(CF)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 39, 22, 9, 27, 27, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 1, 1, 27, 27, 27, 27, 27, 27, 5, 1, 1, 8, 8, 1, 1, 27, 27] 40 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280134 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280134/1 /scratch/stefan/7769901/working/building/REAL300000280134 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/192 `/scratch/stefan/7769901/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(CF)C=C2)C=C1) `REAL300000280134.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280134 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(CF)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 29, 29, 29, 41, 29, 29, 1, 1, 2, 2, 1, 1, 29, 29, 41, 41, 29, 29, 1, 1] 41 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280134 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(CF)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [37, 29, 37, 9, 9, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 8, 8, 1, 1, 29, 29] 41 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 17, 20, 21, 22, 23, 24, 25, 33, 28, 29]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280134 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280134 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280134/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280134/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280134 Building REAL300000280135 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280135' /scratch/stefan/7769901/working/building/REAL300000280135 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280135 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280135/0 /scratch/stefan/7769901/working/building/REAL300000280135 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/193 `/scratch/stefan/7769901/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C(F)(F)F)SC=C2)C=C1) `REAL300000280135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280135 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C(F)(F)F)SC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 1, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280135 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(C(F)(F)F)SC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 17, 17] 17 rigid atoms, others: [9, 12, 13, 14, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280135 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280135 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280135/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280135 Building REAL300000280136 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280136' /scratch/stefan/7769901/working/building/REAL300000280136 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280136 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280136/0 /scratch/stefan/7769901/working/building/REAL300000280136 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/194 `/scratch/stefan/7769901/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=C2)C=C1) `REAL300000280136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280136 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280136 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 25, 25, 25, 25, 25, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280136 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280136/1 /scratch/stefan/7769901/working/building/REAL300000280136 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/195 `/scratch/stefan/7769901/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC(C(F)(F)F)=C2)C=C1) `REAL300000280136.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280136 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 7, 25, 25, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280136 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 25, 25, 25, 25, 25, 9, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280136 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280136 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280136/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280136/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280136 Building REAL300000280137 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280137' /scratch/stefan/7769901/working/building/REAL300000280137 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280137 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280137/0 /scratch/stefan/7769901/working/building/REAL300000280137 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/196 `/scratch/stefan/7769901/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280137 none CC1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 17, 29, 29, 20, 29, 37, 37, 37, 29, 29, 1, 2, 2, 2, 2, 2, 2, 29, 29, 37, 37, 29, 29, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280137 none CC1=NN(C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 1, 1, 29] 37 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280137 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280137 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280137/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280137 Building REAL300000280138 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280138' /scratch/stefan/7769901/working/building/REAL300000280138 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280138 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280138/0 /scratch/stefan/7769901/working/building/REAL300000280138 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/197 `/scratch/stefan/7769901/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(F)(F)CC2)C=C1) `REAL300000280138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280138 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(F)(F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 49, 49, 49, 49, 49, 49, 49, 1, 1, 2, 2, 1, 1, 11, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 20, 21, 24, 25, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280138 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(F)(F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 21, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 49 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280138 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280138 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280138/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280138 Building REAL300000280139 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280139' /scratch/stefan/7769901/working/building/REAL300000280139 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280139 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280139/0 /scratch/stefan/7769901/working/building/REAL300000280139 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/198 `/scratch/stefan/7769901/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=C2)C=C1) `REAL300000280139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280139 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 1, 7, 22, 22, 22, 1, 1] 22 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280139 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 17, 22, 22, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 22, 22] 22 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280139 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280139/1 /scratch/stefan/7769901/working/building/REAL300000280139 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/199 `/scratch/stefan/7769901/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=C2)C=C1) `REAL300000280139.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280139 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25, 1, 1] 25 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280139 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)C(Cl)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 20, 18, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280139 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280139 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280139/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280139/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280139 Building REAL300000280140 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280140' /scratch/stefan/7769901/working/building/REAL300000280140 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280140 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280140/0 /scratch/stefan/7769901/working/building/REAL300000280140 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/200 `/scratch/stefan/7769901/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1C) `REAL300000280140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280140 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 5, 15, 15, 15, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 5, 13, 13, 15, 15, 13, 13, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280140 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 3, 3, 1, 1, 13, 13, 13] 15 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280140 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280140/1 /scratch/stefan/7769901/working/building/REAL300000280140 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/201 `/scratch/stefan/7769901/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C) `REAL300000280140.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280140 none CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 5, 13, 13, 9, 13, 16, 16, 16, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 16, 16, 13, 13, 2, 2, 2] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280140 none CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 3, 3, 1, 1, 13, 13, 13] 16 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280140 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280140 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280140/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280140/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280140 Building REAL300000280141 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280141' /scratch/stefan/7769901/working/building/REAL300000280141 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280141 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280141/0 /scratch/stefan/7769901/working/building/REAL300000280141 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/202 `/scratch/stefan/7769901/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C(F)F)C=C1) `REAL300000280141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280141 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 39, 39, 39, 39, 39, 39, 45, 45, 1, 1, 2, 2, 1, 1, 39, 39, 39, 39, 45, 1, 1] 45 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280141 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [41, 39, 41, 27, 27, 39, 39, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 5, 39, 39] 45 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280141 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280141/1 /scratch/stefan/7769901/working/building/REAL300000280141 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/203 `/scratch/stefan/7769901/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C(F)F)C=C1) `REAL300000280141.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280141 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 45, 45, 45, 45, 45, 45, 55, 55, 1, 1, 2, 2, 1, 1, 11, 45, 45, 45, 45, 55, 1, 1] 55 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280141 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 21, 21, 45, 45, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 45, 45, 45, 45, 45, 45, 11, 1, 1, 1, 1, 6, 45, 45] 55 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280141 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280141 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280141/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280141/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280141 Building REAL300000280142 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280142' /scratch/stefan/7769901/working/building/REAL300000280142 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280142 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280142/0 /scratch/stefan/7769901/working/building/REAL300000280142 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/204 `/scratch/stefan/7769901/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280142 none CCCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [61, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 11, 11, 23, 45, 45, 13, 13, 1, 69, 69, 69, 69, 69, 51, 51, 1, 1, 1, 9, 13, 13, 23, 23, 13, 13, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 24, 42] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280142 none CCCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [194, 158, 76, 13, 76, 13, 13, 13, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 13, 194, 194, 194, 194, 194, 158, 158, 13, 13, 13, 4, 1, 1, 2, 2, 1, 1, 13] 201 rigid atoms, others: [36, 37, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42]) total number of confs: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280142 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280142/1 /scratch/stefan/7769901/working/building/REAL300000280142 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/205 `/scratch/stefan/7769901/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280142.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280142 none CCCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 14, 33, 48, 48, 19, 19, 1, 61, 61, 61, 61, 61, 46, 46, 1, 1, 1, 19, 19, 33, 33, 19, 19, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 41, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280142 none CCCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 164, 85, 19, 85, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 190, 190, 190, 190, 190, 164, 164, 19, 19, 19, 1, 1, 2, 2, 1, 1, 19] 201 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280142 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280142 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280142/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280142/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280142 Building REAL300000280143 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280143' /scratch/stefan/7769901/working/building/REAL300000280143 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280143 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280143/0 /scratch/stefan/7769901/working/building/REAL300000280143 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/206 `/scratch/stefan/7769901/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CCC2)C=C1) `REAL300000280143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280143 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 2, 2, 1, 1, 13, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1] 111 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 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]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280143 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 87, 85, 111, 111, 42, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111] 111 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 10, 11, 42, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 460 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280143 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280143 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280143/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280143 Building REAL300000280144 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280144' /scratch/stefan/7769901/working/building/REAL300000280144 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280144 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280144/0 /scratch/stefan/7769901/working/building/REAL300000280144 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/207 `/scratch/stefan/7769901/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OC(=O)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280144 none CC1(C)OC(=O)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 12, 12, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 40, 32, 23, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280144 none CC1(C)OC(=O)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 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, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 2, 2, 1, 1, 15, 15] 15 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280144 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280144/1 /scratch/stefan/7769901/working/building/REAL300000280144 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/208 `/scratch/stefan/7769901/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OC(=O)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280144.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280144 none CC1(C)OC(=O)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 32, 23, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280144 none CC1(C)OC(=O)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17, 17] 17 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280144 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280144 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280144/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280144/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280144 Building REAL300000280145 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280145' /scratch/stefan/7769901/working/building/REAL300000280145 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280145 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280145/0 /scratch/stefan/7769901/working/building/REAL300000280145 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/209 `/scratch/stefan/7769901/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(Cl)=CC=C3OC2)C=C1) `REAL300000280145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280145 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(Cl)=CC=C3OC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 36, 36, 36, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 2, 2, 1, 1, 13, 105, 105, 105, 105, 105, 105, 1, 1] 105 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280145 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC(Cl)=CC=C3OC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 76, 76, 105, 105, 39, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 39, 1, 1, 1, 1, 1, 1, 105, 105] 105 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280145 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280145 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280145/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280145 Building REAL300000280146 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280146' /scratch/stefan/7769901/working/building/REAL300000280146 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280146 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280146/0 /scratch/stefan/7769901/working/building/REAL300000280146 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/210 `/scratch/stefan/7769901/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(OC(F)F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280146 none N#CC1=CC=C(OC(F)F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 3, 3, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 10, 11, 35, 25, 26, 27] set([7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280146 none N#CC1=CC=C(OC(F)F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 5, 5, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 5, 5, 5, 5, 1, 1, 2, 2, 1, 1, 5] 5 rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280146 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280146/1 /scratch/stefan/7769901/working/building/REAL300000280146 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/211 `/scratch/stefan/7769901/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(OC(F)F)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280146.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280146 none N#CC1=CC=C(OC(F)F)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 22, 22, 1, 1, 7, 7, 7, 10, 14, 14, 12, 14, 18, 24, 24, 14, 14, 1, 1, 1, 22, 10, 14, 14, 18, 18, 14, 14, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 10, 11, 25, 26, 27, 36] set([7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280146 none N#CC1=CC=C(OC(F)F)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 20, 24, 24, 8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 14, 14, 14, 24, 4, 1, 1, 3, 3, 1, 1, 14] 24 rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280146 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280146 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280146/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280146/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280146 Building REAL300000280147 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280147' /scratch/stefan/7769901/working/building/REAL300000280147 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280147 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280147/0 /scratch/stefan/7769901/working/building/REAL300000280147 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/212 `/scratch/stefan/7769901/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280147 none CC(=O)OCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [44, 32, 44, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 19, 35, 64, 64, 19, 19, 1, 1, 44, 44, 44, 4, 4, 1, 1, 9, 19, 19, 35, 35, 19, 19, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280147 none CC(=O)OCC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [166, 162, 166, 66, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 19, 166, 166, 166, 66, 66, 19, 19, 4, 1, 1, 2, 2, 1, 1, 19, 19] 201 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280147 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280147/1 /scratch/stefan/7769901/working/building/REAL300000280147 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/213 `/scratch/stefan/7769901/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280147.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280147 none CC(=O)OCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 51, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 15, 20, 37, 59, 59, 21, 21, 1, 1, 52, 52, 52, 4, 4, 1, 1, 21, 21, 37, 37, 21, 21, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 38, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280147 none CC(=O)OCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 172, 183, 65, 21, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 21, 21, 183, 183, 183, 65, 65, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21] 201 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280147 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280147 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280147/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280147/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280147 Building REAL300000280148 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280148' /scratch/stefan/7769901/working/building/REAL300000280148 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280148 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280148/0 /scratch/stefan/7769901/working/building/REAL300000280148 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/214 `/scratch/stefan/7769901/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl) `REAL300000280148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280148 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 13, 13, 21, 21, 21, 17, 17, 1, 1, 1, 1, 1, 17, 17, 21, 21, 17, 17] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280148 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1] 21 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280148 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280148/1 /scratch/stefan/7769901/working/building/REAL300000280148 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/215 `/scratch/stefan/7769901/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1Cl) `REAL300000280148.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280148 none N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 15, 15, 12, 12, 19, 19, 19, 15, 15, 1, 1, 1, 1, 1, 7, 15, 15, 19, 19, 15, 15] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280148 none N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 15, 15, 15, 15, 15, 6, 1, 1, 2, 2, 1, 1] 19 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280148 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280148 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280148/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280148/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280148 Building REAL300000280149 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280149' /scratch/stefan/7769901/working/building/REAL300000280149 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280149 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280149/0 /scratch/stefan/7769901/working/building/REAL300000280149 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/216 `/scratch/stefan/7769901/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=C2)C=C1) `REAL300000280149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 50, 18, 12, 18, 18, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 79, 79, 79, 79, 79, 79, 12, 12, 1, 1, 1, 1, 12, 79, 79] 79 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 36, 36, 36, 36, 79, 79, 79, 79, 79, 79, 36, 36, 1, 1, 2, 2, 1, 1, 36, 36, 79, 79, 79, 79, 36, 1, 1] 79 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 25, 26, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 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: [50, 36, 50, 36, 36, 36, 36, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 36, 36, 36, 36, 36, 36, 1, 1, 7, 7, 7, 7, 1, 36, 36] 79 rigid atoms, others: [32, 37, 9, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280149 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280149/1 /scratch/stefan/7769901/working/building/REAL300000280149 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/217 `/scratch/stefan/7769901/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=C2)C=C1) `REAL300000280149.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 63, 64, 64, 42, 18, 9, 18, 18, 9, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 64, 64, 64, 64, 64, 42, 10, 10, 1, 1, 1, 1, 10, 64, 64] 64 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 32, 32, 32, 32, 64, 64, 64, 64, 64, 64, 32, 32, 1, 1, 2, 2, 1, 1, 7, 32, 32, 64, 64, 64, 64, 32, 1, 1] 64 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280149 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(N3C(=O)CCC3=O)N=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 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: [46, 32, 46, 17, 17, 32, 32, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 32, 32, 32, 32, 32, 32, 9, 1, 1, 7, 7, 7, 7, 1, 32, 32] 64 rigid atoms, others: [32, 33, 38, 9, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 39, 40]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280149 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280149 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280149/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280149/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280149 Building REAL300000280150 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280150' /scratch/stefan/7769901/working/building/REAL300000280150 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280150 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280150/0 /scratch/stefan/7769901/working/building/REAL300000280150 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/218 `/scratch/stefan/7769901/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)(F)F)C=C1) `REAL300000280150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280150 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17, 17, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280150 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 1, 1, 17, 17] 17 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280150 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280150 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280150/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280150 Building REAL300000280151 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280151' /scratch/stefan/7769901/working/building/REAL300000280151 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280151 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280151/0 /scratch/stefan/7769901/working/building/REAL300000280151 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/219 `/scratch/stefan/7769901/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3)=C2)C=C1) `REAL300000280151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 74, 76, 83, 83, 42, 17, 10, 17, 17, 10, 1, 10, 10, 1, 1, 1, 1, 10, 83, 83, 83, 83, 83, 83, 42, 3, 10, 10, 1, 1, 1, 1, 1, 10, 83, 83] 83 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 287 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 34, 34, 18, 34, 34, 83, 83, 34, 1, 1, 2, 2, 1, 1, 9, 34, 34, 18, 83, 83, 83, 83, 83, 34, 1, 1] 83 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [45, 34, 45, 17, 17, 34, 34, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 1, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 10, 10, 10, 10, 10, 1, 34, 34] 83 rigid atoms, others: [36, 9, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 247 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280151 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280151/1 /scratch/stefan/7769901/working/building/REAL300000280151 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/220 `/scratch/stefan/7769901/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3)=C2)C=C1) `REAL300000280151.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [84, 84, 84, 73, 79, 84, 84, 42, 17, 10, 17, 17, 10, 2, 10, 10, 1, 1, 1, 1, 10, 84, 84, 84, 84, 84, 84, 3, 10, 10, 1, 1, 1, 1, 1, 10, 84, 84] 84 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 258 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 39, 39, 32, 39, 39, 84, 84, 39, 1, 1, 2, 2, 1, 1, 39, 39, 39, 84, 84, 84, 84, 84, 39, 1, 1] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 37, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 309 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280151 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [44, 39, 44, 19, 18, 39, 39, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 10, 10, 10, 10, 10, 1, 39, 39] 84 rigid atoms, others: [35, 9, 12, 13, 14, 15, 16, 17, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 249 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280151 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280151 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280151/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280151/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280151 Building REAL300000280152 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280152' /scratch/stefan/7769901/working/building/REAL300000280152 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280152 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280152/0 /scratch/stefan/7769901/working/building/REAL300000280152 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/221 `/scratch/stefan/7769901/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CS1) `REAL300000280152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280152 none COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 1, 1, 1, 7, 7, 7, 25, 56, 56, 37, 56, 81, 87, 87, 56, 56, 1, 1, 1, 8, 8, 8, 56, 56, 81, 81, 56, 56, 1, 1] 89 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 30, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280152 none COC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 56, 56, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 56, 56, 56, 74, 74, 74, 1, 1, 3, 3, 1, 1, 56, 56] 89 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280152 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280152 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280152/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280152 Building REAL300000280153 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280153' /scratch/stefan/7769901/working/building/REAL300000280153 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280153 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280153/0 /scratch/stefan/7769901/working/building/REAL300000280153 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/222 `/scratch/stefan/7769901/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1) `REAL300000280153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280153 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 1, 1] 17 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280153 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 17 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280153 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280153/1 /scratch/stefan/7769901/working/building/REAL300000280153 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/223 `/scratch/stefan/7769901/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1) `REAL300000280153.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280153 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 1, 1] 15 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280153 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(F)=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 15, 15, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 15, 15] 15 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280153 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280153 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280153/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280153/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280153 Building REAL300000280154 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280154' /scratch/stefan/7769901/working/building/REAL300000280154 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280154 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280154/0 /scratch/stefan/7769901/working/building/REAL300000280154 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/224 `/scratch/stefan/7769901/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280154 none COC(=O)C1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 49, 49, 79, 87, 87, 49, 49, 1, 13, 13, 13, 1, 1, 1, 49, 49, 79, 79, 49, 49, 1] 109 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280154 none COC(=O)C1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [91, 91, 49, 91, 49, 49, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 49, 91, 91, 91, 49, 49, 49, 1, 1, 2, 2, 1, 1, 49] 109 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280154 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280154 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280154/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280154 Building REAL300000280155 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280155' /scratch/stefan/7769901/working/building/REAL300000280155 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280155 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280155/0 /scratch/stefan/7769901/working/building/REAL300000280155 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/225 `/scratch/stefan/7769901/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1) `REAL300000280155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 111, 111, 125, 125, 69, 35, 8, 35, 35, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 125, 125, 125, 125, 125, 125, 8, 8, 1, 1, 1, 1, 1, 8, 125, 125] 125 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 403 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 71, 71, 44, 71, 125, 125, 71, 71, 71, 1, 1, 2, 2, 1, 1, 71, 71, 125, 125, 125, 125, 125, 71, 1, 1] 125 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [93, 71, 93, 38, 39, 71, 71, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 71, 71, 71, 71, 71, 71, 1, 1, 8, 8, 8, 8, 8, 1, 71, 71] 125 rigid atoms, others: [35, 9, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 432 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280155 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280155/1 /scratch/stefan/7769901/working/building/REAL300000280155 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/226 `/scratch/stefan/7769901/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1) `REAL300000280155.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 110, 110, 111, 111, 65, 33, 9, 33, 33, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 111, 111, 111, 111, 111, 111, 65, 9, 9, 1, 1, 1, 1, 1, 9, 111, 111] 111 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 63, 63, 41, 63, 111, 111, 63, 63, 63, 1, 1, 2, 2, 1, 1, 10, 63, 63, 111, 111, 111, 111, 111, 63, 1, 1] 111 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 22, 23, 26, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 441 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280155 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [80, 63, 80, 40, 40, 63, 63, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 63, 63, 63, 63, 63, 63, 21, 1, 1, 9, 9, 9, 9, 9, 1, 63, 63] 111 rigid atoms, others: [36, 9, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 367 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280155 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280155 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280155/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280155/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280155 Building REAL300000280156 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280156' /scratch/stefan/7769901/working/building/REAL300000280156 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280156 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280156/0 /scratch/stefan/7769901/working/building/REAL300000280156 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/227 `/scratch/stefan/7769901/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCCC2)C=C1) `REAL300000280156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280156 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 43, 15, 6, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81] 81 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40]) total number of confs: 155 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280156 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 68, 68, 68, 68, 68, 81, 81, 81, 81, 1, 1, 2, 2, 1, 1, 68, 68, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1] 81 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280156 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [70, 68, 70, 68, 68, 68, 68, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 68, 68, 68, 68, 68, 68, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 68, 68] 81 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280156 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280156 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280156/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280156 Building REAL300000280157 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280157' /scratch/stefan/7769901/working/building/REAL300000280157 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280157 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280157/0 /scratch/stefan/7769901/working/building/REAL300000280157 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/228 `/scratch/stefan/7769901/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280157 none CCC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 57, 57, 57, 57, 94, 124, 124, 57, 57, 7, 7, 7, 7, 7, 3, 4, 4, 4, 1, 1, 57, 57, 94, 94, 57, 57] 131 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9] set([0, 1, 3, 10, 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]) total number of confs: 478 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280157 none CCC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [95, 83, 57, 83, 57, 57, 57, 57, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 97, 97, 97, 97, 97, 83, 83, 83, 83, 57, 57, 1, 1, 2, 2, 1, 1] 131 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 365 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280157 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280157 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280157/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280157 Building REAL300000280158 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280158' /scratch/stefan/7769901/working/building/REAL300000280158 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280158 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280158/0 /scratch/stefan/7769901/working/building/REAL300000280158 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/229 `/scratch/stefan/7769901/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280158 none CNC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 6, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 15, 19, 35, 49, 49, 19, 19, 1, 1, 14, 14, 14, 14, 6, 1, 1, 9, 19, 19, 35, 35, 19, 19, 1, 1] 109 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280158 none CNC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [96, 82, 68, 82, 19, 19, 19, 19, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 19, 96, 96, 96, 96, 68, 19, 19, 6, 1, 1, 2, 2, 1, 1, 19, 19] 109 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280158 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280158/1 /scratch/stefan/7769901/working/building/REAL300000280158 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/230 `/scratch/stefan/7769901/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280158.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280158 none CNC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 14, 14, 30, 32, 32, 19, 19, 1, 1, 8, 8, 8, 8, 6, 1, 1, 19, 19, 30, 30, 19, 19, 1, 1] 59 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 38, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280158 none CNC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 55, 55, 55, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 19, 19, 59, 59, 59, 59, 55, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19] 59 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280158 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280158 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280158/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280158/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280158 Building REAL300000280159 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280159' /scratch/stefan/7769901/working/building/REAL300000280159 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280159 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280159/0 /scratch/stefan/7769901/working/building/REAL300000280159 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/231 `/scratch/stefan/7769901/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280159 none CS(=O)(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 19, 34, 34, 25, 34, 34, 34, 34, 34, 34, 1, 3, 3, 3, 1, 34, 34, 34, 34, 34, 34, 1] 42 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 22, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280159 none CS(=O)(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 34, 42, 42, 34, 34, 34, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 34, 42, 42, 42, 34, 1, 1, 3, 3, 1, 1, 34] 42 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280159 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280159 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280159/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280159 Building REAL300000280160 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280160' /scratch/stefan/7769901/working/building/REAL300000280160 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280160 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280160/0 /scratch/stefan/7769901/working/building/REAL300000280160 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/232 `/scratch/stefan/7769901/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2C=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C2=N1) `REAL300000280160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280160 none CN1N=C2C=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C2=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 25, 51, 51, 36, 37, 59, 59, 59, 51, 51, 1, 1, 2, 2, 2, 1, 1, 1, 51, 51, 59, 59, 51, 51] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280160 none CN1N=C2C=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C2=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 51, 51, 51, 51, 51, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 2, 2, 1, 1] 59 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280160 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280160 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280160/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280160 Building REAL300000280161 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280161' /scratch/stefan/7769901/working/building/REAL300000280161 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280161 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280161/0 /scratch/stefan/7769901/working/building/REAL300000280161 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/233 `/scratch/stefan/7769901/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1) `REAL300000280161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280161 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 63, 63, 37, 63, 99, 115, 115, 63, 63, 1, 9, 9, 9, 9, 9, 1, 1, 63, 63, 99, 99, 63, 63] 149 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280161 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [128, 63, 63, 63, 63, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 63, 128, 128, 128, 128, 128, 63, 63, 1, 1, 2, 2, 1, 1] 149 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280161 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280161 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280161/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280161 Building REAL300000280162 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280162' /scratch/stefan/7769901/working/building/REAL300000280162 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280162 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280162/0 /scratch/stefan/7769901/working/building/REAL300000280162 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/234 `/scratch/stefan/7769901/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280162 none COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 33, 33, 26, 26, 45, 51, 51, 33, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 33, 33, 45, 45, 33, 33] 77 rigid atoms, others: [32, 33, 2, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 31] set([0, 1, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280162 none COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 33, 57, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 57, 57, 57, 33, 33, 33, 33, 33, 33, 1, 1, 2, 2, 1, 1] 77 rigid atoms, others: [37, 38, 41, 42, 17, 18, 19, 20, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280162 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280162/1 /scratch/stefan/7769901/working/building/REAL300000280162 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/235 `/scratch/stefan/7769901/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280162.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280162 none COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 14, 14, 29, 31, 31, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 1, 9, 19, 19, 29, 29, 19, 19] 55 rigid atoms, others: [32, 33, 2, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 31] set([0, 1, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280162 none COC(=O)C1=CC2=CC=CC=C2C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 19, 37, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 37, 37, 37, 19, 19, 19, 19, 19, 19, 6, 1, 1, 2, 2, 1, 1] 55 rigid atoms, others: [38, 39, 42, 43, 17, 18, 19, 20, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280162 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280162 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280162/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280162/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280162 Building REAL300000280163 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280163' /scratch/stefan/7769901/working/building/REAL300000280163 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280163 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280163/0 /scratch/stefan/7769901/working/building/REAL300000280163 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/236 `/scratch/stefan/7769901/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)O2)C=C1) `REAL300000280163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280163 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 51, 51, 1, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280163 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 39, 51, 51, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 51, 51, 51, 51, 51, 51, 1, 1, 51, 51] 51 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280163 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280163 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280163/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280163 Building REAL300000280164 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280164' /scratch/stefan/7769901/working/building/REAL300000280164 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280164 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280164/0 /scratch/stefan/7769901/working/building/REAL300000280164 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/237 `/scratch/stefan/7769901/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280164 none COC1=CC(F)=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 47, 47, 34, 47, 66, 68, 68, 47, 47, 4, 4, 4, 1, 1, 47, 47, 66, 66, 47, 47] 68 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280164 none COC1=CC(F)=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [55, 47, 47, 47, 29, 28, 47, 47, 47, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 55, 55, 55, 47, 47, 1, 1, 2, 2, 1, 1] 68 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280164 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280164/1 /scratch/stefan/7769901/working/building/REAL300000280164 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/238 `/scratch/stefan/7769901/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280164.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280164 none COC1=CC(F)=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 39, 49, 72, 72, 72, 49, 49, 4, 4, 4, 1, 1, 25, 49, 49, 72, 72, 49, 49] 72 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280164 none COC1=CC(F)=C(F)C=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [66, 49, 49, 49, 29, 30, 49, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 66, 66, 66, 49, 49, 6, 1, 1, 2, 2, 1, 1] 72 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280164 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280164 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280164/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280164/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280164 Building REAL300000280165 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280165' /scratch/stefan/7769901/working/building/REAL300000280165 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280165 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280165/0 /scratch/stefan/7769901/working/building/REAL300000280165 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/239 `/scratch/stefan/7769901/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCOCC2)=N1) `REAL300000280165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280165 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 15, 15, 15, 43, 84, 84, 64, 64, 100, 100, 100, 84, 84, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 84, 84, 100, 100, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280165 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 61, 61, 35, 35, 93, 93, 93, 61, 61, 1, 1, 4, 4, 4, 4, 4, 1, 2, 2, 2, 1, 61, 61, 93, 93, 61, 61, 4, 4, 4, 4, 4, 4, 4, 4, 4] 100 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280165 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 61, 61, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 61, 61, 84, 84, 84, 84, 84, 61, 61, 61, 61, 61, 1, 1, 2, 2, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84] 100 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280165 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280165 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280165/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280165 Building REAL300000280166 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280166' /scratch/stefan/7769901/working/building/REAL300000280166 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280166 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280166/0 /scratch/stefan/7769901/working/building/REAL300000280166 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/240 `/scratch/stefan/7769901/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280166 none CC(F)(F)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 13, 13, 33, 49, 49, 18, 18, 1, 13, 13, 13, 1, 1, 1, 9, 18, 18, 33, 33, 18, 18, 1] 69 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280166 none CC(F)(F)C1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [62, 18, 62, 62, 18, 18, 18, 18, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 18, 62, 62, 62, 18, 18, 18, 5, 1, 1, 2, 2, 1, 1, 18] 69 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280166 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280166/1 /scratch/stefan/7769901/working/building/REAL300000280166 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/241 `/scratch/stefan/7769901/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280166.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280166 none CC(F)(F)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 13, 13, 29, 37, 37, 19, 19, 1, 10, 10, 10, 1, 1, 1, 19, 19, 29, 29, 19, 19, 1] 57 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280166 none CC(F)(F)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 19, 53, 53, 19, 19, 19, 19, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 19, 53, 53, 53, 19, 19, 19, 1, 1, 2, 2, 1, 1, 19] 57 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280166 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280166 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280166/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280166/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280166 Building REAL300000280167 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280167' /scratch/stefan/7769901/working/building/REAL300000280167 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280167 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280167/0 /scratch/stefan/7769901/working/building/REAL300000280167 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/242 `/scratch/stefan/7769901/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC(F)F)=C2)C=C1) `REAL300000280167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280167 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 18, 21, 21, 7, 1, 1, 2, 2, 1, 1, 6, 7, 7, 7, 21, 7, 1, 1] 21 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280167 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 15, 3, 3, 7, 7, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 16, 16, 1, 7, 7, 7, 7, 7, 7, 3, 1, 1, 1, 16, 1, 7, 7] 21 rigid atoms, others: [33, 9, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280167 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280167/1 /scratch/stefan/7769901/working/building/REAL300000280167 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/243 `/scratch/stefan/7769901/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC(F)F)=C2)C=C1) `REAL300000280167.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280167 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 13, 13, 7, 1, 1, 2, 2, 1, 1, 7, 7, 7, 13, 7, 1, 1] 13 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280167 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [9, 7, 9, 3, 3, 7, 7, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 13, 1, 7, 7] 13 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 33, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280167 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280167 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280167/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280167/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280167 Building REAL300000280168 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280168' /scratch/stefan/7769901/working/building/REAL300000280168 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280168 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280168/0 /scratch/stefan/7769901/working/building/REAL300000280168 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/244 `/scratch/stefan/7769901/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C3=CC=CC=C3)CC2)C=C1) `REAL300000280168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280168 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 95, 87, 109, 109, 45, 15, 4, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 109, 109, 109, 109, 109, 109, 45, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 109, 109] 109 rigid atoms, others: [36, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 404 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280168 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 105, 105, 105, 105, 109, 109, 106, 109, 109, 105, 105, 1, 1, 2, 2, 1, 1, 13, 105, 105, 105, 105, 105, 109, 109, 109, 109, 109, 105, 105, 105, 105, 1, 1] 109 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: 240 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280168 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 105, 109, 51, 48, 105, 105, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 105, 105, 105, 105, 105, 105, 25, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 105, 105] 109 rigid atoms, others: [32, 33, 34, 35, 9, 42, 43, 12, 13, 14, 15, 16, 41, 22, 23, 44, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 589 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280168 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280168 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280168/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280168 Building REAL300000280169 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280169' /scratch/stefan/7769901/working/building/REAL300000280169 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280169 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280169/0 /scratch/stefan/7769901/working/building/REAL300000280169 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/245 `/scratch/stefan/7769901/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1) `REAL300000280169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280169 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 53, 53, 28, 25, 87, 96, 96, 53, 53, 1, 13, 13, 13, 1, 1, 53, 53, 87, 87, 53, 53] 100 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280169 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [91, 53, 53, 53, 53, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 53, 91, 91, 91, 53, 53, 1, 1, 3, 3, 1, 1] 100 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280169 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280169 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280169/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280169 Building REAL300000280170 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280170' /scratch/stefan/7769901/working/building/REAL300000280170 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280170 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280170/0 /scratch/stefan/7769901/working/building/REAL300000280170 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/246 `/scratch/stefan/7769901/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12) `REAL300000280170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280170 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 15, 15, 13, 9, 27, 27, 27, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 27, 27, 15, 15, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 41, 20, 21, 22, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280170 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 3, 3, 1, 1, 15, 15, 15] 27 rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280170 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280170/1 /scratch/stefan/7769901/working/building/REAL300000280170 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/247 `/scratch/stefan/7769901/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12) `REAL300000280170.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280170 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 17, 17, 9, 9, 25, 25, 25, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 17, 17, 25, 25, 17, 17, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 42, 20, 21, 22, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280170 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 3, 3, 1, 1, 17, 17, 17] 25 rigid atoms, others: [34, 35, 38, 39, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280170 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280170 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280170/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280170/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280170 Building REAL300000280171 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280171' /scratch/stefan/7769901/working/building/REAL300000280171 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280171 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280171/0 /scratch/stefan/7769901/working/building/REAL300000280171 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/248 `/scratch/stefan/7769901/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C(F)(F)F)CC2)C=C1) `REAL300000280171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280171 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C(F)(F)F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 1, 1, 11, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1] 59 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 39, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280171 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCC(C(F)(F)F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 59, 59, 59, 59, 59, 59, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280171 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280171 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280171/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280171 Building REAL300000280172 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280172' /scratch/stefan/7769901/working/building/REAL300000280172 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280172 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280172/0 /scratch/stefan/7769901/working/building/REAL300000280172 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/249 `/scratch/stefan/7769901/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CCF)N=C2)C=C1) `REAL300000280172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280172 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CCF)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 43, 43, 43, 123, 125, 43, 43, 1, 1, 2, 2, 1, 1, 43, 123, 123, 125, 125, 43, 1, 1] 125 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280172 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(CCF)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [71, 43, 71, 43, 43, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 9, 25, 1, 1, 43, 43, 43, 43, 43, 43, 1, 9, 9, 25, 25, 1, 43, 43] 125 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280172 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280172 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280172/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280172 Building REAL300000280173 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280173' /scratch/stefan/7769901/working/building/REAL300000280173 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280173 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280173/0 /scratch/stefan/7769901/working/building/REAL300000280173 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/250 `/scratch/stefan/7769901/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280173 none CCOCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [53, 37, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 12, 12, 29, 61, 61, 15, 15, 1, 54, 54, 54, 53, 53, 8, 8, 1, 1, 1, 9, 15, 15, 29, 29, 15, 15, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 41, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280173 none CCOCC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [191, 173, 95, 15, 15, 15, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 15, 191, 191, 191, 191, 191, 95, 95, 15, 15, 15, 4, 1, 1, 2, 2, 1, 1, 15] 201 rigid atoms, others: [35, 36, 39, 40, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280173 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280173/1 /scratch/stefan/7769901/working/building/REAL300000280173 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/251 `/scratch/stefan/7769901/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280173.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280173 none CCOCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 32, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 29, 43, 43, 17, 17, 1, 38, 38, 38, 38, 38, 8, 8, 1, 1, 1, 17, 17, 29, 29, 17, 17, 1] 152 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 40, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280173 none CCOCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [148, 144, 87, 17, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 148, 148, 148, 148, 148, 87, 87, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17] 152 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280173 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280173 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280173/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280173/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280173 Building REAL300000280174 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280174' /scratch/stefan/7769901/working/building/REAL300000280174 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280174 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280174/0 /scratch/stefan/7769901/working/building/REAL300000280174 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/252 `/scratch/stefan/7769901/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(CCl)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl) `REAL300000280174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280174 none CN1N=C(CCl)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'Cl', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 1, 1, 11, 11, 11, 25, 61, 61, 61, 61, 100, 108, 108, 61, 61, 1, 1, 2, 2, 2, 6, 6, 61, 61, 100, 100, 61, 61] 115 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 21, 22] set([5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280174 none CN1N=C(CCl)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'Cl', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 61, 61, 61, 61, 84, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 61, 61, 61, 61, 61, 84, 84, 1, 1, 2, 2, 1, 1] 115 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280174 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280174 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280174/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280174 Building REAL300000280175 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280175' /scratch/stefan/7769901/working/building/REAL300000280175 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280175 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280175/0 /scratch/stefan/7769901/working/building/REAL300000280175 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/253 `/scratch/stefan/7769901/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2=CC=CC=C2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280175 none CN1N=C(C2=CC=CC=C2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 57, 57, 57, 90, 90, 57, 90, 90, 57, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 57, 57, 57, 90, 90, 57, 90, 90, 57, 1, 1, 2, 2, 1, 1] 106 rigid atoms, others: [35, 36, 39, 40, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 270 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280175 none CN1N=C(C2=CC=CC=C2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 1, 6, 6, 1, 1, 1, 7, 7, 7, 23, 57, 57, 38, 38, 86, 90, 90, 57, 57, 2, 2, 2, 7, 7, 1, 7, 7, 1, 57, 57, 86, 86, 57, 57] 106 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 34] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280175 none CN1N=C(C2=CC=CC=C2)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 33, 33, 68, 90, 90, 87, 88, 106, 106, 106, 90, 90, 7, 7, 7, 1, 1, 1, 1, 1, 7, 90, 90, 106, 106, 90, 90] 106 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280175 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280175 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280175/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280175 Building REAL300000280176 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280176' /scratch/stefan/7769901/working/building/REAL300000280176 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280176 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280176/0 /scratch/stefan/7769901/working/building/REAL300000280176 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/254 `/scratch/stefan/7769901/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCCC3)N=C2)C=C1) `REAL300000280176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280176 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 118, 122, 122, 78, 25, 13, 25, 25, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 122, 122, 122, 122, 122, 122, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 122, 122] 122 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 41, 42, 43]) total number of confs: 261 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280176 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 42, 42, 42, 122, 122, 122, 122, 122, 42, 42, 1, 1, 2, 2, 1, 1, 42, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 42, 1, 1] 122 rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 43, 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]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280176 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN(C3CCCCC3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 42, 52, 17, 17, 42, 42, 9, 2, 1, 2, 2, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 42, 42, 42, 42, 42, 42, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 42, 42] 122 rigid atoms, others: [9, 12, 13, 14, 15, 21, 22, 41, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280176 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280176 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280176/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280176 Building REAL300000280177 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280177' /scratch/stefan/7769901/working/building/REAL300000280177 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280177 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280177/0 /scratch/stefan/7769901/working/building/REAL300000280177 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/255 `/scratch/stefan/7769901/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3=CC=CC=C3)C=C2)C=C1) `REAL300000280177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280177 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3=CC=CC=C3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 139, 165, 165, 73, 19, 5, 19, 19, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 165, 165, 165, 165, 165, 165, 73, 19, 19, 1, 1, 1, 1, 1, 19, 19, 165, 165] 165 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280177 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3=CC=CC=C3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 26, 131, 165, 165, 131, 165, 165, 26, 26, 1, 1, 2, 2, 1, 1, 11, 26, 26, 165, 165, 131, 165, 165, 26, 26, 1, 1] 165 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280177 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3=CC=CC=C3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 26, 34, 16, 9, 26, 26, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 19, 19, 9, 19, 19, 1, 1, 26, 26, 26, 26, 26, 26, 5, 1, 1, 19, 19, 9, 19, 19, 1, 1, 26, 26] 165 rigid atoms, others: [32, 33, 39, 40, 9, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280177 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280177 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280177/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280177 Building REAL300000280178 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280178' /scratch/stefan/7769901/working/building/REAL300000280178 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280178 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280178/0 /scratch/stefan/7769901/working/building/REAL300000280178 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/256 `/scratch/stefan/7769901/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2CF)C=C1) `REAL300000280178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280178 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2CF)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 51, 51, 51, 51, 51, 51, 53, 1, 1, 2, 2, 1, 1, 9, 51, 51, 51, 51, 53, 53, 1, 1] 53 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280178 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2CF)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 51, 53, 29, 29, 51, 51, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 51, 51, 51, 51, 51, 51, 13, 1, 1, 1, 1, 6, 6, 51, 51] 53 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280178 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280178/1 /scratch/stefan/7769901/working/building/REAL300000280178 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/257 `/scratch/stefan/7769901/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2CF)C=C1) `REAL300000280178.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280178 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2CF)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 1, 1] 37 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280178 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2CF)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 2, 2, 37, 37] 37 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280178 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280178 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280178/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280178/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280178 Building REAL300000280179 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280179' /scratch/stefan/7769901/working/building/REAL300000280179 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280179 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280179/0 /scratch/stefan/7769901/working/building/REAL300000280179 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/258 `/scratch/stefan/7769901/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280179 none CCOC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [70, 33, 31, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 19, 19, 14, 14, 31, 47, 47, 19, 19, 70, 70, 70, 70, 70, 6, 6, 1, 1, 1, 1, 7, 19, 19, 31, 31, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 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]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280179 none CCOC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [171, 116, 116, 45, 116, 19, 19, 19, 19, 19, 19, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 171, 171, 171, 171, 171, 45, 45, 19, 19, 19, 19, 6, 1, 1, 3, 3, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280179 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280179/1 /scratch/stefan/7769901/working/building/REAL300000280179 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/259 `/scratch/stefan/7769901/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280179.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280179 none CCOC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 25, 6, 25, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 20, 20, 37, 54, 54, 25, 25, 54, 54, 54, 54, 54, 6, 6, 1, 1, 1, 1, 25, 25, 37, 37, 25, 25] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 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: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280179 none CCOC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 114, 55, 114, 25, 25, 25, 25, 25, 25, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 183, 183, 183, 183, 183, 55, 55, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [37, 38, 41, 42, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280179 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280179 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280179/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280179/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280179 Building REAL300000280180 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280180' /scratch/stefan/7769901/working/building/REAL300000280180 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280180 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280180/0 /scratch/stefan/7769901/working/building/REAL300000280180 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/260 `/scratch/stefan/7769901/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br) `REAL300000280180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280180 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 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, 3, 3, 3, 6, 11, 11, 8, 8, 13, 13, 13, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 11, 11, 13, 13, 11, 11, 1, 2, 2, 2] 13 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280180 none CC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11] 13 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280180 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280180/1 /scratch/stefan/7769901/working/building/REAL300000280180 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/261 `/scratch/stefan/7769901/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br) `REAL300000280180.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280180 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 1, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280180 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 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, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15] 15 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280180 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280180 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280180/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280180/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280180 Building REAL300000280181 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280181' /scratch/stefan/7769901/working/building/REAL300000280181 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280181 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280181/0 /scratch/stefan/7769901/working/building/REAL300000280181 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/262 `/scratch/stefan/7769901/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3C=CC=CN23)C=C1) `REAL300000280181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280181 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3C=CC=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43, 43, 1, 1] 43 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280181 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C3C=CC=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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, 40, 43, 43, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 43, 43] 43 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280181 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280181 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280181/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280181 Building REAL300000280182 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280182' /scratch/stefan/7769901/working/building/REAL300000280182 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280182 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280182/0 /scratch/stefan/7769901/working/building/REAL300000280182 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/263 `/scratch/stefan/7769901/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3SC=NC3=C2)C=C1) `REAL300000280182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280182 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3SC=NC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 1, 7, 22, 22, 22, 22, 1, 1] 22 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280182 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3SC=NC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 22, 22] 22 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280182 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280182/1 /scratch/stefan/7769901/working/building/REAL300000280182 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/264 `/scratch/stefan/7769901/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3SC=NC3=C2)C=C1) `REAL300000280182.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280182 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3SC=NC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280182 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3SC=NC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280182 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280182 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280182/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280182/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280182 Building REAL300000280183 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280183' /scratch/stefan/7769901/working/building/REAL300000280183 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280183 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280183/0 /scratch/stefan/7769901/working/building/REAL300000280183 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/265 `/scratch/stefan/7769901/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1) `REAL300000280183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280183 none CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 60, 60, 34, 60, 90, 100, 100, 60, 60, 1, 9, 9, 9, 9, 9, 1, 60, 60, 90, 90, 60, 60] 143 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280183 none CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [121, 60, 60, 60, 60, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 60, 121, 121, 121, 121, 121, 60, 1, 1, 2, 2, 1, 1] 143 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280183 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280183 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280183/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280183 Building REAL300000280184 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280184' /scratch/stefan/7769901/working/building/REAL300000280184 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280184 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280184/0 /scratch/stefan/7769901/working/building/REAL300000280184 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/266 `/scratch/stefan/7769901/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl) `REAL300000280184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280184 none CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 51, 51, 51, 51, 71, 77, 77, 51, 51, 1, 1, 6, 6, 6, 6, 6, 1, 51, 51, 71, 71, 51, 51] 105 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280184 none CCN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [91, 51, 51, 51, 51, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 91, 91, 91, 91, 91, 51, 1, 1, 2, 2, 1, 1] 105 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280184 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280184 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280184/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280184 Building REAL300000280185 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280185' /scratch/stefan/7769901/working/building/REAL300000280185 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280185 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280185/0 /scratch/stefan/7769901/working/building/REAL300000280185 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/267 `/scratch/stefan/7769901/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Br)C=C1) `REAL300000280185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280185 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 31, 31, 31, 151, 151, 201, 201, 195, 201, 201, 201, 1, 1, 2, 2, 1, 1, 13, 151, 151, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 531 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280185 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 126, 53, 9, 53, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 126, 9, 9, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 525 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280185 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280185 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280185/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280185 Building REAL300000280186 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280186' /scratch/stefan/7769901/working/building/REAL300000280186 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280186 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280186/0 /scratch/stefan/7769901/working/building/REAL300000280186 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/268 `/scratch/stefan/7769901/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)N=C2F)C=C1) `REAL300000280186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280186 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)N=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1, 38, 38, 1, 1] 38 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280186 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(F)(F)F)N=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 38, 38, 38, 38, 38, 38, 1, 1, 38, 38] 38 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280186 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280186 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280186/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280186 Building REAL300000280187 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280187' /scratch/stefan/7769901/working/building/REAL300000280187 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280187 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280187/0 /scratch/stefan/7769901/working/building/REAL300000280187 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/269 `/scratch/stefan/7769901/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=CN=C(Cl)C=C32)C=C1) `REAL300000280187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280187 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280187 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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 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, 23, 23, 45, 45, 15, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 24, 25, 26, 27, 28, 29]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280187 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280187 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280187/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280187 Building REAL300000280188 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280188' /scratch/stefan/7769901/working/building/REAL300000280188 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280188 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280188/0 /scratch/stefan/7769901/working/building/REAL300000280188 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/270 `/scratch/stefan/7769901/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)O2)C=C1) `REAL300000280188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280188 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 27, 27, 27, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280188 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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, 29, 39, 39, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 39, 39] 39 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280188 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280188 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280188/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280188 Building REAL300000280189 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280189' /scratch/stefan/7769901/working/building/REAL300000280189 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280189 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280189/0 /scratch/stefan/7769901/working/building/REAL300000280189 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/271 `/scratch/stefan/7769901/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1) `REAL300000280189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280189 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 9, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280189 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280189 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280189/1 /scratch/stefan/7769901/working/building/REAL300000280189 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/272 `/scratch/stefan/7769901/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1) `REAL300000280189.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280189 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280189 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC3=CN=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 17, 25, 25, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 23, 24, 25, 26, 27, 28]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280189 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280189 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280189/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280189/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280189 Building REAL300000280190 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280190' /scratch/stefan/7769901/working/building/REAL300000280190 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280190 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280190/0 /scratch/stefan/7769901/working/building/REAL300000280190 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/273 `/scratch/stefan/7769901/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12) `REAL300000280190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280190 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 15, 15, 12, 13, 19, 19, 19, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 15, 15, 19, 19, 15, 15, 1, 1, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 19, 20, 21, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280190 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15] 19 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280190 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280190/1 /scratch/stefan/7769901/working/building/REAL300000280190 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/274 `/scratch/stefan/7769901/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12) `REAL300000280190.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280190 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 7, 15, 15, 11, 11, 21, 21, 21, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 21, 21, 15, 15, 1, 1, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 23, 24, 36, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280190 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15] 21 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280190 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280190 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280190/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280190/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280190 Building REAL300000280191 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280191' /scratch/stefan/7769901/working/building/REAL300000280191 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280191 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280191/0 /scratch/stefan/7769901/working/building/REAL300000280191 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/275 `/scratch/stefan/7769901/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OCCF)C=C2)C=C1) `REAL300000280191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280191 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OCCF)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 11, 33, 63, 63, 11, 11, 1, 1, 2, 2, 1, 1, 9, 11, 11, 63, 63, 63, 63, 11, 11, 1, 1] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 22, 23, 26, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 217 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280191 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OCCF)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 11, 17, 5, 5, 11, 11, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 19, 29, 1, 1, 11, 11, 11, 11, 11, 11, 3, 1, 1, 19, 19, 29, 29, 1, 1, 11, 11] 63 rigid atoms, others: [35, 36, 9, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 37, 38]) total number of confs: 198 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280191 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280191 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280191/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280191 Building REAL300000280192 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280192' /scratch/stefan/7769901/working/building/REAL300000280192 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280192 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280192/0 /scratch/stefan/7769901/working/building/REAL300000280192 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/276 `/scratch/stefan/7769901/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280192 none CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 3, 3, 3, 9, 22, 22, 22, 22, 24, 24, 24, 22, 22, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 22, 22, 24, 24, 22, 22, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 25, 24, 36, 26, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280192 none CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 22, 22, 22, 22, 22, 22, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 2, 2, 1, 1, 22, 22] 24 rigid atoms, others: [38, 39, 42, 43, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280192 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280192/1 /scratch/stefan/7769901/working/building/REAL300000280192 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/277 `/scratch/stefan/7769901/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280192.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280192 none CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 44, 25, 24, 36, 26, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280192 none CN1C(=O)C(C)(C)C2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 2, 2, 1, 1, 27, 27] 27 rigid atoms, others: [37, 38, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43, 44]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280192 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280192 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280192/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280192/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280192 Building REAL300000280193 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280193' /scratch/stefan/7769901/working/building/REAL300000280193 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280193 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280193/0 /scratch/stefan/7769901/working/building/REAL300000280193 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/278 `/scratch/stefan/7769901/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2F)C=C1) `REAL300000280193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280193 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 2, 2, 1, 1, 39, 39, 1, 1] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280193 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 39, 39] 39 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280193 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280193 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280193/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280193 Building REAL300000280194 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280194' /scratch/stefan/7769901/working/building/REAL300000280194 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280194 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280194/0 /scratch/stefan/7769901/working/building/REAL300000280194 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/279 `/scratch/stefan/7769901/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(C)(=O)=O)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1) `REAL300000280194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280194 none CC1=C(S(C)(=O)=O)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 6, 6, 6, 23, 51, 51, 33, 51, 67, 67, 67, 51, 51, 1, 2, 2, 2, 7, 7, 7, 1, 51, 51, 67, 67, 51, 51] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23, 30] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280194 none CC1=C(S(C)(=O)=O)C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 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] 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: [51, 51, 51, 51, 72, 72, 72, 51, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 51, 51, 72, 72, 72, 51, 1, 1, 2, 2, 1, 1] 82 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280194 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280194 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280194/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280194 Building REAL300000280195 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280195' /scratch/stefan/7769901/working/building/REAL300000280195 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280195 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280195/0 /scratch/stefan/7769901/working/building/REAL300000280195 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/280 `/scratch/stefan/7769901/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1) `REAL300000280195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280195 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 11, 11, 11, 25, 48, 48, 48, 48, 60, 60, 60, 48, 48, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 60, 60, 48, 48, 1, 1, 1, 1, 1] 60 rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280195 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 21, 42, 42, 42, 42, 60, 60, 60, 42, 42, 1, 1, 4, 4, 1, 4, 4, 1, 2, 2, 2, 1, 42, 42, 60, 60, 42, 42, 4, 4, 1, 4, 4] 60 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280195 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [42, 42, 42, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 42, 42, 48, 48, 43, 48, 48, 42, 42, 42, 42, 42, 1, 1, 2, 2, 1, 1, 48, 48, 42, 48, 48] 60 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280195 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280195 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280195/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280195 Building REAL300000280196 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280196' /scratch/stefan/7769901/working/building/REAL300000280196 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280196 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280196/0 /scratch/stefan/7769901/working/building/REAL300000280196 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/281 `/scratch/stefan/7769901/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(F)C=C2)C=C1) `REAL300000280196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280196 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 157, 157, 173, 173, 173, 173, 173, 173, 1, 1, 2, 2, 1, 1, 13, 157, 157, 173, 173, 173, 173, 1, 1] 173 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 479 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280196 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 172, 173, 173, 110, 50, 6, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 110, 6, 6, 1, 1, 1, 1, 173, 173] 173 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 466 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280196 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280196 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280196/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280196 Building REAL300000280197 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280197' /scratch/stefan/7769901/working/building/REAL300000280197 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280197 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280197/0 /scratch/stefan/7769901/working/building/REAL300000280197 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/282 `/scratch/stefan/7769901/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Br)=C2)C=C1) `REAL300000280197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280197 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Br)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 99, 99, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 9, 99, 99, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280197 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=CC(Br)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 197, 201, 201, 143, 72, 11, 72, 72, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 143, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 596 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280197 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280197 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280197/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280197 Building REAL300000280198 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280198' /scratch/stefan/7769901/working/building/REAL300000280198 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280198 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280198/0 /scratch/stefan/7769901/working/building/REAL300000280198 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/283 `/scratch/stefan/7769901/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Br)C=C2)C=C1) `REAL300000280198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280198 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Br)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 157, 157, 177, 177, 177, 177, 177, 177, 1, 1, 2, 2, 1, 1, 13, 157, 157, 177, 177, 177, 177, 1, 1] 177 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 487 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280198 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Br)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 175, 177, 177, 112, 50, 6, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 112, 6, 6, 1, 1, 1, 1, 177, 177] 177 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 481 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280198 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280198 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280198/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280198 Building REAL300000280199 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280199' /scratch/stefan/7769901/working/building/REAL300000280199 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280199 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280199/0 /scratch/stefan/7769901/working/building/REAL300000280199 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/284 `/scratch/stefan/7769901/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)S2)C=C1) `REAL300000280199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280199 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 162, 162, 174, 174, 119, 51, 13, 51, 51, 13, 13, 13, 1, 1, 1, 1, 13, 174, 174, 174, 174, 174, 174, 13, 13, 1, 1, 1, 1, 1, 174, 174] 174 rigid atoms, others: [32, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 476 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280199 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 84, 84, 84, 84, 174, 174, 84, 1, 1, 2, 2, 1, 1, 84, 84, 174, 174, 174, 174, 174, 1, 1] 174 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280199 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [125, 84, 125, 44, 44, 84, 84, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 13, 13, 1, 84, 84, 84, 84, 84, 84, 1, 1, 13, 13, 13, 13, 13, 84, 84] 174 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280199 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280199 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280199/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280199 Building REAL300000280200 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280200' /scratch/stefan/7769901/working/building/REAL300000280200 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280200 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280200/0 /scratch/stefan/7769901/working/building/REAL300000280200 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/285 `/scratch/stefan/7769901/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-]) `REAL300000280200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280200 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 13, 13, 19, 19, 19, 15, 15, 1, 1, 1, 2, 2, 1, 1, 15, 15, 19, 19, 15, 15, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 21, 22, 25, 26] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280200 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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: [15, 15, 15, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 1, 1, 15] 19 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280200 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280200/1 /scratch/stefan/7769901/working/building/REAL300000280200 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/286 `/scratch/stefan/7769901/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-]) `REAL300000280200.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280200 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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, 3, 3, 3, 9, 16, 16, 13, 13, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 1, 1, 9, 16, 16, 16, 16, 16, 16, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280200 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 2, 2, 1, 1, 16] 16 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280200 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280200 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280200/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280200/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280200 Building REAL300000280201 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280201' /scratch/stefan/7769901/working/building/REAL300000280201 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280201 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280201/0 /scratch/stefan/7769901/working/building/REAL300000280201 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/287 `/scratch/stefan/7769901/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C(C)S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280201 none COC1=CC=C(C=C(C)S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 37, 37, 91, 151, 151, 124, 151, 185, 185, 185, 151, 151, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 91, 151, 151, 185, 185, 151, 151, 1, 1] 185 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 710 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280201 none COC1=CC=C(C=C(C)S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [151, 145, 143, 151, 151, 103, 103, 19, 103, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 151, 151, 151, 151, 151, 151, 151, 103, 103, 103, 103, 7, 1, 1, 2, 2, 1, 1, 151, 151] 185 rigid atoms, others: [35, 36, 39, 40, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42]) total number of confs: 419 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280201 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280201 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280201/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280201 Building REAL300000280202 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280202' /scratch/stefan/7769901/working/building/REAL300000280202 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280202 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280202/0 /scratch/stefan/7769901/working/building/REAL300000280202 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/288 `/scratch/stefan/7769901/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=NS2)C=C1) `REAL300000280202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280202 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=NS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 69, 1, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280202 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Br)C=NS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 27, 36, 69, 69, 27, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 1, 69, 69] 69 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280202 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280202 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280202/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280202 Building REAL300000280203 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280203' /scratch/stefan/7769901/working/building/REAL300000280203 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280203 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280203/0 /scratch/stefan/7769901/working/building/REAL300000280203 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/289 `/scratch/stefan/7769901/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C=CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280203 none COC(=O)C=CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 3, 15, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 19, 28, 48, 64, 64, 29, 29, 1, 1, 15, 15, 15, 3, 3, 1, 1, 9, 29, 29, 48, 48, 29, 29, 1, 1] 108 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 40, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 310 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280203 none COC(=O)C=CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [99, 92, 48, 99, 48, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 99, 99, 99, 48, 48, 29, 29, 6, 1, 1, 2, 2, 1, 1, 29, 29] 108 rigid atoms, others: [34, 35, 38, 39, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) total number of confs: 348 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280203 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280203/1 /scratch/stefan/7769901/working/building/REAL300000280203 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/290 `/scratch/stefan/7769901/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280203.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280203 none COC(=O)C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 3, 15, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 17, 17, 51, 63, 63, 29, 29, 1, 1, 15, 15, 15, 3, 3, 1, 1, 29, 29, 51, 51, 29, 29, 1, 1] 113 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 39, 40, 24, 25, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 300 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280203 none COC(=O)C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 101, 51, 113, 51, 29, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 113, 113, 113, 51, 51, 29, 29, 1, 1, 2, 2, 1, 1, 29, 29] 113 rigid atoms, others: [33, 34, 37, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40]) total number of confs: 457 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280203 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280203 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280203/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280203/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280203 Building REAL300000280204 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280204' /scratch/stefan/7769901/working/building/REAL300000280204 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280204 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280204/0 /scratch/stefan/7769901/working/building/REAL300000280204 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/291 `/scratch/stefan/7769901/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=NN1) `REAL300000280204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280204 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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: [48, 20, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 25, 59, 59, 39, 59, 89, 114, 114, 59, 59, 1, 1, 48, 48, 48, 47, 47, 1, 59, 59, 89, 89, 59, 59, 1] 192 rigid atoms, others: [3, 36, 5, 6, 7, 8, 22, 23, 29] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280204 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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: [184, 149, 119, 59, 119, 59, 59, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 59, 59, 184, 184, 184, 184, 184, 59, 1, 1, 2, 2, 1, 1, 59] 192 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280204 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280204 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280204/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280204 Building REAL300000280205 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280205' /scratch/stefan/7769901/working/building/REAL300000280205 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280205 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280205/0 /scratch/stefan/7769901/working/building/REAL300000280205 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/292 `/scratch/stefan/7769901/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC) `REAL300000280205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280205 none COC1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 40, 86, 86, 62, 62, 132, 158, 158, 86, 86, 1, 1, 5, 4, 4, 4, 1, 86, 86, 132, 132, 86, 86, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 663 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280205 none COC1=CSC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 86, 86, 86, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 86, 86, 139, 151, 151, 151, 86, 1, 1, 2, 2, 1, 1, 139, 139, 139] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35]) total number of confs: 382 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280205 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280205 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280205/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280205 Building REAL300000280206 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280206' /scratch/stefan/7769901/working/building/REAL300000280206 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280206 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280206/0 /scratch/stefan/7769901/working/building/REAL300000280206 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/293 `/scratch/stefan/7769901/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1) `REAL300000280206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280206 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 9, 21, 21, 1, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280206 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 11, 1, 1, 21, 21] 21 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280206 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280206/1 /scratch/stefan/7769901/working/building/REAL300000280206 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/294 `/scratch/stefan/7769901/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1) `REAL300000280206.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280206 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 19, 19, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280206 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C([O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 19, 19] 19 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280206 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280206 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280206/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280206/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280206 Building REAL300000280207 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280207' /scratch/stefan/7769901/working/building/REAL300000280207 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280207 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280207/0 /scratch/stefan/7769901/working/building/REAL300000280207 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/295 `/scratch/stefan/7769901/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(F)C(Cl)=C2)C=C1) `REAL300000280207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280207 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(F)C(Cl)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21, 1, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280207 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=C(F)C(Cl)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 9, 14, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 21, 21] 21 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280207 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280207/1 /scratch/stefan/7769901/working/building/REAL300000280207 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/296 `/scratch/stefan/7769901/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C(F)C(Cl)=C2)C=C1) `REAL300000280207.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280207 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C(F)C(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 1, 7, 22, 22, 1, 1] 22 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280207 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=C(F)C(Cl)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 20, 18, 22, 22, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 9, 1, 1, 22, 22] 22 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280207 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280207 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280207/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280207/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280207 Building REAL300000280208 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280208' /scratch/stefan/7769901/working/building/REAL300000280208 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280208 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280208/0 /scratch/stefan/7769901/working/building/REAL300000280208 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/297 `/scratch/stefan/7769901/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1) `REAL300000280208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280208 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 1, 1] 5 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280208 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 5, 3, 3] 5 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280208 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280208/1 /scratch/stefan/7769901/working/building/REAL300000280208 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/298 `/scratch/stefan/7769901/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1) `REAL300000280208.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280208 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 1, 1, 2, 5, 5, 5, 5, 1, 1] 5 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280208 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280208 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280208 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280208/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280208/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280208 Building REAL300000280209 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280209' /scratch/stefan/7769901/working/building/REAL300000280209 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280209 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280209/0 /scratch/stefan/7769901/working/building/REAL300000280209 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/299 `/scratch/stefan/7769901/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(OC(F)F)=C2)C=C1) `REAL300000280209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280209 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(OC(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 21, 21, 7, 1, 1, 2, 2, 1, 1, 6, 7, 7, 21, 7, 1, 1] 21 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280209 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(OC(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 14, 3, 3, 7, 7, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 1, 7, 7, 7, 7, 7, 7, 3, 1, 1, 15, 1, 7, 7] 21 rigid atoms, others: [33, 9, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280209 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280209/1 /scratch/stefan/7769901/working/building/REAL300000280209 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/300 `/scratch/stefan/7769901/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(OC(F)F)=C2)C=C1) `REAL300000280209.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280209 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(OC(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 15, 15, 7, 1, 1, 2, 2, 1, 1, 7, 7, 15, 7, 1, 1] 15 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280209 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(OC(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 3, 3, 7, 7, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 1, 7, 7, 7, 7, 7, 7, 1, 1, 15, 1, 7, 7] 15 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 33, 34]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280209 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280209 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280209/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280209/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280209 Building REAL300000280210 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280210' /scratch/stefan/7769901/working/building/REAL300000280210 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280210 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280210/0 /scratch/stefan/7769901/working/building/REAL300000280210 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/301 `/scratch/stefan/7769901/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2C=CC=CC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280210 none CN1N=C2C=CC=CC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 41, 41, 35, 36, 62, 62, 62, 41, 41, 2, 2, 2, 1, 1, 1, 1, 41, 41, 62, 62, 41, 41] 62 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([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: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280210 none CN1N=C2C=CC=CC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 41, 41, 41, 41, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 41, 41, 41, 41, 41, 41, 41, 1, 1, 2, 2, 1, 1] 62 rigid atoms, others: [32, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280210 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280210 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280210/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280210 Building REAL300000280211 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280211' /scratch/stefan/7769901/working/building/REAL300000280211 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280211 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280211/0 /scratch/stefan/7769901/working/building/REAL300000280211 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/302 `/scratch/stefan/7769901/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280211 none CN1C=CC2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 22, 22, 22, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 17, 17, 22, 22, 17, 17, 1, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280211 none CN1C=CC2=CC(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 17, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 2, 2, 1, 1, 17, 17] 22 rigid atoms, others: [32, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280211 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280211/1 /scratch/stefan/7769901/working/building/REAL300000280211 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/303 `/scratch/stefan/7769901/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21) `REAL300000280211.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280211 none CN1C=CC2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 24, 24, 24, 24, 25, 25, 25, 24, 24, 1, 1, 1, 2, 2, 2, 1, 1, 1, 24, 24, 25, 25, 24, 24, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280211 none CN1C=CC2=CC(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 24, 24, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 2, 2, 1, 1, 24, 24] 25 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280211 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280211 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280211/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280211/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280211 Building REAL300000280212 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280212' /scratch/stefan/7769901/working/building/REAL300000280212 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280212 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280212/0 /scratch/stefan/7769901/working/building/REAL300000280212 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/304 `/scratch/stefan/7769901/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1) `REAL300000280212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280212 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 1, 1] 17 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280212 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 17, 17, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 17 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280212 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280212/1 /scratch/stefan/7769901/working/building/REAL300000280212 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/305 `/scratch/stefan/7769901/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1) `REAL300000280212.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280212 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 1, 1] 15 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280212 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 15, 15] 15 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280212 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280212 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280212/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280212/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280212 Building REAL300000280213 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280213' /scratch/stefan/7769901/working/building/REAL300000280213 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280213 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280213/0 /scratch/stefan/7769901/working/building/REAL300000280213 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/306 `/scratch/stefan/7769901/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C3OCCCOC3=C2)C=C1) `REAL300000280213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280213 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C3OCCCOC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280213 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C3OCCCOC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 40, 39, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280213 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280213/1 /scratch/stefan/7769901/working/building/REAL300000280213 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/307 `/scratch/stefan/7769901/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C3OCCCOC3=C2)C=C1) `REAL300000280213.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280213 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C3OCCCOC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 24, 25, 38, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280213 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C3OCCCOC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 15, 16, 16, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280213 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280213 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280213/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280213/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280213 Building REAL300000280214 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280214' /scratch/stefan/7769901/working/building/REAL300000280214 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280214 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280214/0 /scratch/stefan/7769901/working/building/REAL300000280214 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/308 `/scratch/stefan/7769901/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C(Cl)S2)C=C1) `REAL300000280214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280214 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 51, 51, 51, 51, 51, 51, 1, 1, 2, 2, 1, 1, 51, 1, 1] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 23, 24, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280214 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 1, 51, 51] 51 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280214 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280214 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280214/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280214 Building REAL300000280215 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280215' /scratch/stefan/7769901/working/building/REAL300000280215 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280215 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280215/0 /scratch/stefan/7769901/working/building/REAL300000280215 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/309 `/scratch/stefan/7769901/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl) `REAL300000280215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280215 none CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 19, 35, 35, 35, 35, 41, 41, 41, 35, 35, 1, 1, 2, 2, 2, 1, 35, 35, 41, 41, 35, 35] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280215 none CN1N=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [35, 35, 35, 35, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 2, 2, 1, 1] 41 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280215 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280215 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280215/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280215 Building REAL300000280216 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280216' /scratch/stefan/7769901/working/building/REAL300000280216 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280216 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280216/0 /scratch/stefan/7769901/working/building/REAL300000280216 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/310 `/scratch/stefan/7769901/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280216 none CC1=NN(C2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 55, 55, 55, 69, 69, 69, 69, 69, 55, 55, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 55, 55, 55, 69, 69, 69, 69, 69, 55, 55, 55, 1, 1, 2, 2, 1, 1] 100 rigid atoms, others: [38, 39, 42, 43, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 150 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280216 none CC1=NN(C2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 3, 4, 4, 1, 1, 1, 1, 10, 10, 10, 22, 55, 55, 34, 30, 98, 98, 98, 55, 55, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 55, 55, 98, 98, 55, 55] 100 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 451 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280216 none CC1=NN(C2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 20, 20, 41, 69, 69, 53, 53, 100, 100, 100, 69, 69, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 69, 69, 100, 100, 69, 69] 100 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 424 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280216 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280216 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280216/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280216 Building REAL300000280217 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280217' /scratch/stefan/7769901/working/building/REAL300000280217 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280217 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280217/0 /scratch/stefan/7769901/working/building/REAL300000280217 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/311 `/scratch/stefan/7769901/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)C(F)F)C=C2)C=C1) `REAL300000280217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280217 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)C(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 118, 118, 138, 138, 20, 20, 1, 1, 2, 2, 1, 1, 9, 20, 20, 138, 20, 20, 1, 1] 138 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280217 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)C(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 20, 42, 9, 9, 20, 20, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 13, 13, 67, 67, 1, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 67, 1, 1, 20, 20] 138 rigid atoms, others: [33, 34, 9, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280217 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280217/1 /scratch/stefan/7769901/working/building/REAL300000280217 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/312 `/scratch/stefan/7769901/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)C(F)F)C=C2)C=C1) `REAL300000280217.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280217 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)C(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 25, 25, 5, 5, 1, 1, 2, 2, 1, 1, 5, 5, 25, 5, 5, 1, 1] 25 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280217 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)C(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 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: [9, 5, 9, 3, 3, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 23, 1, 1, 5, 5] 25 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 35, 34, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280217 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280217 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280217/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280217/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280217 Building REAL300000280218 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280218' /scratch/stefan/7769901/working/building/REAL300000280218 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280218 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280218/0 /scratch/stefan/7769901/working/building/REAL300000280218 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/313 `/scratch/stefan/7769901/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=C2)C=C1) `REAL300000280218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 117, 37, 19, 37, 37, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 117, 19, 19, 19, 1, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 32, 32, 32, 32, 32, 171, 201, 201, 171, 201, 201, 32, 1, 1, 2, 2, 1, 1, 7, 32, 32, 32, 201, 201, 201, 201, 201, 32, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 17, 17, 32, 32, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 9, 19, 19, 9, 19, 19, 1, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1, 19, 19, 12, 19, 19, 1, 32, 32] 201 rigid atoms, others: [32, 33, 34, 40, 9, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280218 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280218/1 /scratch/stefan/7769901/working/building/REAL300000280218 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/314 `/scratch/stefan/7769901/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=C2)C=C1) `REAL300000280218.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 127, 37, 19, 37, 37, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 19, 19, 19, 1, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 31, 31, 31, 31, 31, 165, 201, 201, 165, 201, 201, 31, 1, 1, 2, 2, 1, 1, 31, 31, 31, 201, 201, 201, 201, 201, 31, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280218 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(OC3=CC=CC=C3)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 47, 17, 17, 31, 31, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 19, 19, 11, 19, 19, 1, 31, 31] 201 rigid atoms, others: [32, 33, 39, 9, 12, 13, 14, 15, 16, 17, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280218 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280218 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280218/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280218/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280218 Building REAL300000280219 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280219' /scratch/stefan/7769901/working/building/REAL300000280219 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280219 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280219/0 /scratch/stefan/7769901/working/building/REAL300000280219 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/315 `/scratch/stefan/7769901/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280219 none CC(F)(F)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 18, 18, 14, 14, 26, 27, 27, 18, 18, 5, 5, 5, 1, 1, 1, 1, 18, 18, 26, 26, 18, 18] 39 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280219 none CC(F)(F)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 18, 28, 28, 18, 18, 15, 18, 18, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 28, 28, 28, 18, 16, 18, 18, 1, 1, 2, 2, 1, 1] 39 rigid atoms, others: [32, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280219 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280219/1 /scratch/stefan/7769901/working/building/REAL300000280219 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/316 `/scratch/stefan/7769901/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280219.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280219 none CC(F)(F)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 11, 11, 11, 11, 21, 21, 21, 11, 11, 4, 4, 4, 1, 1, 1, 1, 7, 11, 11, 21, 21, 11, 11] 41 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280219 none CC(F)(F)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 21, 21, 11, 11, 11, 11, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 21, 21, 21, 11, 11, 11, 11, 6, 1, 1, 2, 2, 1, 1] 41 rigid atoms, others: [32, 33, 36, 37, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280219 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280219 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280219/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280219/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280219 Building REAL300000280220 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280220' /scratch/stefan/7769901/working/building/REAL300000280220 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280220 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280220/0 /scratch/stefan/7769901/working/building/REAL300000280220 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/317 `/scratch/stefan/7769901/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1) `REAL300000280220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280220 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 34, 68, 68, 61, 64, 117, 117, 117, 68, 68, 1, 1, 1, 68, 68, 117, 117, 68, 68, 1, 1] 117 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280220 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)OC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 68, 68, 68, 1, 1, 2, 2, 1, 1, 68, 68] 117 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280220 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280220 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280220/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280220 Building REAL300000280221 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280221' /scratch/stefan/7769901/working/building/REAL300000280221 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280221 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280221/0 /scratch/stefan/7769901/working/building/REAL300000280221 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/318 `/scratch/stefan/7769901/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=C2)C=C1) `REAL300000280221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280221 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 5, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 24, 25, 28, 29, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280221 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 17, 17] 17 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280221 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280221/1 /scratch/stefan/7769901/working/building/REAL300000280221 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/319 `/scratch/stefan/7769901/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=C2)C=C1) `REAL300000280221.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280221 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280221 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)C(F)(F)C3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 24, 25, 26, 27, 28, 29]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280221 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280221 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280221/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280221/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280221 Building REAL300000280222 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280222' /scratch/stefan/7769901/working/building/REAL300000280222 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280222 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280222/0 /scratch/stefan/7769901/working/building/REAL300000280222 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/320 `/scratch/stefan/7769901/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C3=NSN=C32)C=C1) `REAL300000280222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280222 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C3=NSN=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 14, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 2, 2, 1, 1, 45, 45, 1, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280222 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C3=NSN=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 14, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 35, 35, 45, 45, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 1, 1, 45, 45] 45 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280222 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280222 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280222/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280222 Building REAL300000280223 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280223' /scratch/stefan/7769901/working/building/REAL300000280223 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280223 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280223/0 /scratch/stefan/7769901/working/building/REAL300000280223 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/321 `/scratch/stefan/7769901/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1) `REAL300000280223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280223 none CCC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 38, 38, 31, 28, 61, 61, 61, 38, 38, 1, 2, 2, 2, 2, 2, 1, 2, 2, 2, 38, 38, 61, 61, 38, 38] 61 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280223 none CCC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 4, 4, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1] 61 rigid atoms, others: [34, 35, 38, 39, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280223 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280223/1 /scratch/stefan/7769901/working/building/REAL300000280223 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/322 `/scratch/stefan/7769901/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1) `REAL300000280223.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280223 none CCC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [69, 34, 12, 34, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 36, 36, 26, 36, 38, 54, 54, 36, 36, 1, 69, 69, 69, 69, 69, 2, 2, 2, 36, 36, 38, 38, 36, 36] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280223 none CCC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [198, 191, 132, 191, 36, 36, 36, 36, 36, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 36, 198, 198, 198, 198, 198, 36, 36, 36, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [33, 34, 37, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280223 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280223 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280223/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280223/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280223 Building REAL300000280224 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280224' /scratch/stefan/7769901/working/building/REAL300000280224 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280224 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280224/0 /scratch/stefan/7769901/working/building/REAL300000280224 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/323 `/scratch/stefan/7769901/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280224 none CC1=CC(Cl)=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 16, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 19, 27, 27, 23, 24, 33, 33, 33, 27, 27, 2, 2, 2, 1, 1, 27, 27, 33, 33, 27, 27] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280224 none CC1=CC(Cl)=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 16, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 27, 27, 27, 27, 27, 1, 1, 2, 2, 1, 1] 33 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280224 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280224/1 /scratch/stefan/7769901/working/building/REAL300000280224 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/324 `/scratch/stefan/7769901/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=NC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280224.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280224 none CC1=CC(Cl)=NC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 16, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 23, 23, 20, 20, 29, 29, 29, 23, 23, 2, 2, 2, 1, 1, 13, 23, 23, 29, 29, 23, 23] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280224 none CC1=CC(Cl)=NC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 16, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 23, 23, 23, 23, 23, 6, 1, 1, 2, 2, 1, 1] 29 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280224 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280224 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280224/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280224/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280224 Building REAL300000280225 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280225' /scratch/stefan/7769901/working/building/REAL300000280225 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280225 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280225/0 /scratch/stefan/7769901/working/building/REAL300000280225 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/325 `/scratch/stefan/7769901/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280225 none C=C(C)COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [60, 26, 60, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 32, 57, 57, 17, 17, 1, 60, 60, 60, 60, 60, 26, 26, 1, 1, 1, 9, 17, 17, 32, 32, 17, 17, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 24, 42] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 406 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280225 none C=C(C)COC1=CC=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [179, 149, 179, 71, 17, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 179, 179, 179, 179, 179, 149, 149, 17, 17, 17, 4, 1, 1, 2, 2, 1, 1, 17] 201 rigid atoms, others: [36, 37, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42]) total number of confs: 582 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280225 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280225/1 /scratch/stefan/7769901/working/building/REAL300000280225 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/326 `/scratch/stefan/7769901/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280225.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280225 none C=C(C)COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 62, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 15, 15, 37, 68, 68, 21, 21, 1, 62, 62, 62, 62, 62, 20, 20, 1, 1, 1, 21, 21, 37, 37, 21, 21, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 41, 24] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 444 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280225 none C=C(C)COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 147, 192, 75, 21, 21, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 21, 192, 192, 192, 192, 192, 147, 147, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21] 201 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41]) total number of confs: 621 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280225 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280225 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280225/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280225/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280225 Building REAL300000280226 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280226' /scratch/stefan/7769901/working/building/REAL300000280226 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280226 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280226/0 /scratch/stefan/7769901/working/building/REAL300000280226 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/327 `/scratch/stefan/7769901/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1) `REAL300000280226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280226 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 31, 31, 31, 65, 99, 99, 80, 80, 132, 140, 140, 99, 99, 1, 1, 1, 1, 8, 33, 33, 33, 33, 33, 8, 99, 99, 132, 132, 99, 99, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 649 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280226 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 7, 7, 7, 23, 52, 52, 34, 34, 78, 94, 94, 52, 52, 1, 1, 8, 8, 1, 9, 9, 9, 9, 9, 1, 52, 52, 78, 78, 52, 52, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280226 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 52, 52, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 52, 52, 99, 99, 52, 109, 109, 109, 109, 109, 52, 1, 1, 2, 2, 1, 1, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280226 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280226 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280226/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280226 Building REAL300000280227 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280227' /scratch/stefan/7769901/working/building/REAL300000280227 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280227 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280227/0 /scratch/stefan/7769901/working/building/REAL300000280227 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/328 `/scratch/stefan/7769901/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NSN=C2C=C1) `REAL300000280227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280227 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NSN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 14, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 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, 5, 5, 5, 9, 19, 19, 14, 14, 30, 30, 30, 19, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 30, 30, 19, 19, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 33, 34, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280227 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NSN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 14, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19] 30 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 15, 16, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280227 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280227 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280227/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280227 Building REAL300000280228 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280228' /scratch/stefan/7769901/working/building/REAL300000280228 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280228 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280228/0 /scratch/stefan/7769901/working/building/REAL300000280228 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/329 `/scratch/stefan/7769901/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=C2)C=C1) `REAL300000280228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280228 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 1, 1, 7, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280228 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 25, 25, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280228 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280228/1 /scratch/stefan/7769901/working/building/REAL300000280228 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/330 `/scratch/stefan/7769901/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=C2)C=C1) `REAL300000280228.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280228 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280228 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=C(Cl)C=C3C=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280228 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280228 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280228/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280228/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280228 Building REAL300000280229 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280229' /scratch/stefan/7769901/working/building/REAL300000280229 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280229 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280229/0 /scratch/stefan/7769901/working/building/REAL300000280229 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/331 `/scratch/stefan/7769901/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(=O)NC(=O)N1) `REAL300000280229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280229 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 6, 4, 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, 6, 6, 6, 11, 24, 24, 20, 20, 31, 31, 31, 24, 24, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 24, 31, 31, 24, 24, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 33, 34, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280229 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 6, 4, 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: [24, 24, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 2, 2, 1, 1, 24, 24] 31 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 15, 16, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 73 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280229 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280229 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280229/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280229 Building REAL300000280230 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280230' /scratch/stefan/7769901/working/building/REAL300000280230 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280230 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280230/0 /scratch/stefan/7769901/working/building/REAL300000280230 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/332 `/scratch/stefan/7769901/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1) `REAL300000280230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280230 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 7, 7, 7, 21, 51, 51, 33, 51, 81, 89, 89, 51, 51, 1, 1, 1, 1, 12, 12, 12, 51, 51, 81, 81, 51, 51, 1] 101 rigid atoms, others: [33, 2, 4, 5, 6, 20, 21, 22, 23] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280230 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [83, 83, 51, 83, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 51, 51, 83, 83, 83, 1, 1, 2, 2, 1, 1, 51] 101 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280230 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280230 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280230/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280230 Building REAL300000280231 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280231' /scratch/stefan/7769901/working/building/REAL300000280231 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280231 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280231/0 /scratch/stefan/7769901/working/building/REAL300000280231 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/333 `/scratch/stefan/7769901/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br) `REAL300000280231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280231 none CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 18, 18, 37, 37, 37, 23, 23, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 9, 23, 23, 37, 37, 23, 23, 1, 1] 58 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 36, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280231 none CCC1=CC(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [48, 23, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 23, 23, 23, 23, 48, 48, 48, 48, 48, 23, 6, 1, 1, 2, 2, 1, 1, 23, 23] 58 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280231 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280231/1 /scratch/stefan/7769901/working/building/REAL300000280231 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/334 `/scratch/stefan/7769901/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br) `REAL300000280231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280231 none CCC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 15, 15, 38, 38, 38, 24, 24, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 24, 24, 38, 38, 24, 24, 1, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280231 none CCC1=CC(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 24, 24, 24, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 24, 24, 24, 24, 61, 61, 61, 61, 61, 24, 1, 1, 2, 2, 1, 1, 24, 24] 61 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280231 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280231 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280231/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280231/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280231 Building REAL300000280232 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280232' /scratch/stefan/7769901/working/building/REAL300000280232 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280232 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280232/0 /scratch/stefan/7769901/working/building/REAL300000280232 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/335 `/scratch/stefan/7769901/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCCC2)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280232 none CC1=NN(C2CCCC2)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 5, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 51, 51, 51, 51, 77, 77, 77, 77, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 51, 51, 51, 51, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 2, 2, 1, 1, 51] 84 rigid atoms, others: [37, 38, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280232 none CC1=NN(C2CCCC2)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 5, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 1, 1, 7, 7, 7, 23, 51, 51, 35, 35, 72, 72, 72, 51, 51, 1, 2, 2, 2, 5, 5, 5, 5, 6, 5, 6, 5, 5, 51, 51, 72, 72, 51, 51, 1] 84 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 43, 24] set([5, 6, 7, 8, 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: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280232 none CC1=NN(C2CCCC2)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 5, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 43, 77, 77, 62, 62, 84, 84, 84, 77, 77, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 84, 84, 77, 77, 5] 84 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280232 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280232 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280232/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280232 Building REAL300000280233 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280233' /scratch/stefan/7769901/working/building/REAL300000280233 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280233 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280233/0 /scratch/stefan/7769901/working/building/REAL300000280233 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/336 `/scratch/stefan/7769901/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC=C2)C=C1) `REAL300000280233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280233 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 41, 41, 41, 41, 41, 1, 1, 2, 2, 1, 1, 41, 41, 1, 1] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280233 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 1, 1, 41, 41] 41 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280233 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280233 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280233/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280233 Building REAL300000280234 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280234' /scratch/stefan/7769901/working/building/REAL300000280234 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280234 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280234/0 /scratch/stefan/7769901/working/building/REAL300000280234 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/337 `/scratch/stefan/7769901/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CS2)C=C1) `REAL300000280234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280234 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 47, 47, 47, 47, 47, 1, 1, 2, 2, 1, 1, 47, 47, 1, 1] 47 rigid atoms, others: [3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280234 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(Cl)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 45, 47, 47, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 1, 1, 47, 47] 47 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280234 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280234 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280234/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280234 Building REAL300000280235 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280235' /scratch/stefan/7769901/working/building/REAL300000280235 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280235 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280235/0 /scratch/stefan/7769901/working/building/REAL300000280235 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/338 `/scratch/stefan/7769901/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280235 none COCCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 1, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 19, 39, 39, 29, 29, 65, 90, 90, 39, 39, 1, 25, 25, 25, 11, 11, 7, 7, 1, 1, 4, 4, 4, 39, 39, 65, 65, 39, 39, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 10, 11, 44, 25] set([0, 1, 2, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280235 none COCCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 114, 80, 39, 39, 39, 39, 39, 39, 65, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 39, 171, 171, 171, 114, 114, 80, 80, 39, 39, 65, 65, 65, 1, 1, 2, 2, 1, 1, 39] 201 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280235 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280235/1 /scratch/stefan/7769901/working/building/REAL300000280235 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/339 `/scratch/stefan/7769901/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280235.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280235 none COCCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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: [29, 10, 6, 1, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 17, 33, 33, 25, 25, 55, 82, 82, 33, 33, 1, 30, 30, 30, 10, 10, 6, 6, 1, 1, 4, 4, 4, 17, 33, 33, 55, 55, 33, 33, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 10, 11, 45, 25] set([0, 1, 2, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280235 none COCCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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: [176, 127, 66, 33, 33, 33, 33, 33, 33, 44, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 33, 176, 176, 176, 127, 127, 66, 66, 33, 33, 44, 44, 44, 4, 1, 1, 2, 2, 1, 1, 33] 201 rigid atoms, others: [39, 40, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280235 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280235 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280235/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280235/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280235 Building REAL300000280236 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280236' /scratch/stefan/7769901/working/building/REAL300000280236 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280236 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280236/0 /scratch/stefan/7769901/working/building/REAL300000280236 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/340 `/scratch/stefan/7769901/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1) `REAL300000280236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280236 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 23, 24, 36, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280236 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 13, 21, 21, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 35, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280236 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280236/1 /scratch/stefan/7769901/working/building/REAL300000280236 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/341 `/scratch/stefan/7769901/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1) `REAL300000280236.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280236 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 8, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280236 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 15, 19, 19, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280236 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280236 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280236/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280236/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280236 Building REAL300000280237 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280237' /scratch/stefan/7769901/working/building/REAL300000280237 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280237 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280237/0 /scratch/stefan/7769901/working/building/REAL300000280237 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/342 `/scratch/stefan/7769901/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCOCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280237 none CN1N=C2CCOCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 37, 37, 37, 37, 55, 55, 55, 37, 37, 2, 2, 2, 1, 1, 1, 1, 1, 1, 37, 37, 55, 55, 37, 37] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280237 none CN1N=C2CCOCC2=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 1, 1] 55 rigid atoms, others: [33, 34, 37, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280237 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280237 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280237/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280237 Building REAL300000280238 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280238' /scratch/stefan/7769901/working/building/REAL300000280238 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280238 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280238/0 /scratch/stefan/7769901/working/building/REAL300000280238 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/343 `/scratch/stefan/7769901/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2)C=C1) `REAL300000280238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 54, 55, 57, 57, 23, 12, 6, 12, 12, 6, 6, 1, 6, 6, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 155 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 39, 39, 39, 39, 39, 39, 57, 57, 1, 1, 2, 2, 1, 1, 11, 39, 39, 39, 39, 57, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [40, 39, 40, 33, 30, 39, 39, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39, 39, 39, 39, 39, 39, 13, 1, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39] 57 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280238 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280238/1 /scratch/stefan/7769901/working/building/REAL300000280238 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/344 `/scratch/stefan/7769901/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2)C=C1) `REAL300000280238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 57, 71, 71, 32, 14, 4, 14, 14, 4, 4, 4, 4, 4, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 4, 4, 4, 4, 1, 1, 1, 1, 1, 71, 71] 71 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 204 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 51, 51, 34, 51, 51, 51, 71, 71, 1, 1, 1, 1, 1, 1, 51, 51, 30, 51, 71, 71, 71, 71, 71, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 37, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 259 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280238 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [54, 51, 54, 51, 36, 51, 51, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 4, 4, 4, 4, 4, 51, 51] 71 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280238 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280238 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280238/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280238/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280238 Building REAL300000280239 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280239' /scratch/stefan/7769901/working/building/REAL300000280239 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280239 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280239/0 /scratch/stefan/7769901/working/building/REAL300000280239 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/345 `/scratch/stefan/7769901/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1) `REAL300000280239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280239 none CC1(C)CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 43, 43, 21, 21, 49, 49, 49, 43, 43, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 21, 43, 43, 49, 49, 43, 43, 1, 1, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 20, 21, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280239 none CC1(C)CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43] 49 rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280239 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280239 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280239/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280239 Building REAL300000280240 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280240' /scratch/stefan/7769901/working/building/REAL300000280240 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280240 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280240/0 /scratch/stefan/7769901/working/building/REAL300000280240 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/346 `/scratch/stefan/7769901/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC1CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1) `REAL300000280240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280240 none CC(=O)OCC1CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 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, 5, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 50, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 27, 27, 43, 67, 67, 27, 27, 1, 1, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 19, 27, 27, 43, 43, 27, 27, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 42, 43, 44, 45, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280240 none CC(=O)OCC1CCN(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 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, 5, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 102, 27, 27, 27, 27, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 27, 27, 170, 170, 170, 102, 102, 27, 27, 27, 27, 27, 4, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [36, 37, 40, 41, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44, 45]) total number of confs: 486 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280240 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280240 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280240/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280240 Building REAL300000280241 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280241' /scratch/stefan/7769901/working/building/REAL300000280241 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280241 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280241/0 /scratch/stefan/7769901/working/building/REAL300000280241 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/347 `/scratch/stefan/7769901/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCN(CC(F)F)CC2)C=C1) `REAL300000280241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280241 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCN(CC(F)F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 10, 10, 5, 5, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 9, 9, 10, 5, 5, 5, 5, 1, 1] 10 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280241 none O=C([O-])CC1=CC=C(NS(=O)(=O)N2CCN(CC(F)F)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 5, 5, 5, 5, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 4, 4, 5, 1, 1, 1, 1, 5, 5] 10 rigid atoms, others: [32, 36, 37, 38, 39, 9, 12, 13, 14, 15, 16, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 40, 41]) total number of confs: 36 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280241 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280241 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280241/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280241 Building REAL300000280242 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280242' /scratch/stefan/7769901/working/building/REAL300000280242 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280242 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280242/0 /scratch/stefan/7769901/working/building/REAL300000280242 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/348 `/scratch/stefan/7769901/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=N1) `REAL300000280242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280242 none COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 5, 5, 5, 13, 21, 21, 21, 21, 30, 30, 30, 21, 21, 1, 1, 1, 3, 3, 3, 1, 1, 13, 21, 21, 30, 30, 21, 21, 2, 2, 2] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280242 none COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 21, 21, 21, 25, 25, 25, 21, 21, 6, 1, 1, 2, 2, 1, 1, 21, 21, 21] 30 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280242 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280242/1 /scratch/stefan/7769901/working/building/REAL300000280242 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/349 `/scratch/stefan/7769901/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1) `REAL300000280242.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280242 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 25, 25, 25, 25, 35, 35, 35, 25, 25, 1, 1, 1, 3, 3, 3, 1, 1, 25, 25, 35, 35, 25, 25, 2, 2, 2] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280242 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 25, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 25, 25, 25, 29, 29, 29, 25, 25, 1, 1, 2, 2, 1, 1, 25, 25, 25] 35 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280242 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280242 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280242/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280242/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280242 Building REAL300000280243 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280243' /scratch/stefan/7769901/working/building/REAL300000280243 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280243 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280243/0 /scratch/stefan/7769901/working/building/REAL300000280243 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/350 `/scratch/stefan/7769901/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280243 none COC1=NC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 55, 55, 37, 55, 64, 64, 64, 55, 55, 3, 3, 3, 1, 2, 2, 2, 1, 55, 55, 64, 64, 55, 55] 64 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280243 none COC1=NC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 55, 55, 55, 55, 55, 55, 55, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 61, 61, 61, 55, 55, 55, 55, 55, 1, 1, 2, 2, 1, 1] 64 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280243 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280243 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280243/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280243 Building REAL300000280244 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280244' /scratch/stefan/7769901/working/building/REAL300000280244 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280244 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280244/0 /scratch/stefan/7769901/working/building/REAL300000280244 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/351 `/scratch/stefan/7769901/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3CCOCC3)C=C2)C=C1) `REAL300000280244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280244 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3CCOCC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 86, 36, 17, 36, 36, 13, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 36, 36, 132, 132, 132, 132, 132, 132, 86, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 132, 132] 132 rigid atoms, others: [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, 33, 43, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280244 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3CCOCC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 91, 132, 132, 132, 132, 132, 21, 21, 1, 1, 2, 2, 1, 1, 9, 21, 21, 132, 132, 132, 132, 132, 132, 132, 132, 132, 21, 21, 1, 1] 132 rigid atoms, others: [3, 4, 5, 6, 7, 8, 45, 46, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 331 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280244 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC3CCOCC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 21, 33, 21, 9, 21, 21, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 13, 36, 36, 36, 36, 36, 1, 1, 21, 21, 21, 21, 21, 21, 5, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 21, 21] 132 rigid atoms, others: [32, 33, 9, 43, 12, 13, 14, 15, 16, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 208 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280244 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280244 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280244/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280244 Building REAL300000280245 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280245' /scratch/stefan/7769901/working/building/REAL300000280245 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280245 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280245/0 /scratch/stefan/7769901/working/building/REAL300000280245 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/352 `/scratch/stefan/7769901/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280245 none COC1=NC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 51, 51, 37, 51, 57, 57, 57, 51, 51, 4, 4, 4, 1, 1, 51, 51, 57, 57, 51, 51] 57 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280245 none COC1=NC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [55, 51, 51, 51, 51, 51, 51, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 55, 55, 55, 51, 51, 1, 1, 2, 2, 1, 1] 57 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280245 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280245 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280245/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280245 Building REAL300000280246 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280246' /scratch/stefan/7769901/working/building/REAL300000280246 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280246 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280246/0 /scratch/stefan/7769901/working/building/REAL300000280246 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/353 `/scratch/stefan/7769901/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300000280246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280246 none COC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 29, 33, 33, 17, 17, 1, 1, 1, 4, 4, 4, 1, 9, 17, 17, 29, 29, 17, 17, 1, 2, 2, 2] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280246 none COC1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 17, 17, 17, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 17, 17, 17, 29, 29, 29, 17, 6, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17] 33 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280246 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280246/1 /scratch/stefan/7769901/working/building/REAL300000280246 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/354 `/scratch/stefan/7769901/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300000280246.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280246 none COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 9, 9, 29, 33, 33, 22, 22, 1, 1, 1, 4, 4, 4, 1, 22, 22, 29, 29, 22, 22, 1, 2, 2, 2] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 20, 21, 22, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280246 none COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 22, 22, 22, 22, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 22, 22, 22, 32, 32, 32, 22, 1, 1, 3, 3, 1, 1, 22, 22, 22, 22] 33 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280246 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280246 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280246/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280246/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280246 Building REAL300000280247 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280247' /scratch/stefan/7769901/working/building/REAL300000280247 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280247 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280247/0 /scratch/stefan/7769901/working/building/REAL300000280247 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/355 `/scratch/stefan/7769901/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1) `REAL300000280247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280247 none CC(C)CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 16, 16, 46, 50, 50, 27, 27, 1, 1, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 27, 27, 46, 46, 27, 27, 1] 122 rigid atoms, others: [32, 3, 4, 5, 6, 7, 39, 21, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280247 none CC(C)CN1C=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [116, 91, 116, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 27, 27, 116, 116, 116, 116, 116, 116, 116, 91, 91, 27, 1, 1, 2, 2, 1, 1, 27] 122 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280247 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280247 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280247/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280247 Building REAL300000280248 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280248' /scratch/stefan/7769901/working/building/REAL300000280248 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280248 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280248/0 /scratch/stefan/7769901/working/building/REAL300000280248 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/356 `/scratch/stefan/7769901/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280248 none CC1=NN(C(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 1, 1, 1, 7, 7, 7, 21, 58, 58, 58, 58, 95, 103, 103, 58, 58, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 1, 58, 58, 95, 95, 58, 58] 131 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280248 none CC1=NN(C(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 116, 116, 58, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 58, 58, 58, 116, 116, 116, 116, 116, 116, 116, 58, 1, 1, 2, 2, 1, 1] 131 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280248 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280248 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280248/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280248 Building REAL300000280249 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280249' /scratch/stefan/7769901/working/building/REAL300000280249 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280249 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280249/0 /scratch/stefan/7769901/working/building/REAL300000280249 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/357 `/scratch/stefan/7769901/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=N2)C=C1) `REAL300000280249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280249 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 50, 1, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280249 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CSC(C(F)(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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, 41, 50, 50, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 50, 50, 50, 50, 50, 50, 1, 50, 50] 50 rigid atoms, others: [9, 12, 13, 14, 15, 16, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280249 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280249 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280249/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280249 Building REAL300000280250 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280250' /scratch/stefan/7769901/working/building/REAL300000280250 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280250 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280250/0 /scratch/stefan/7769901/working/building/REAL300000280250 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/358 `/scratch/stefan/7769901/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CO1) `REAL300000280250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280250 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CO1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 7, 7, 7, 20, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 41, 41, 41, 41, 41, 41, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280250 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=CO1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 41, 41, 41, 1, 1, 2, 2, 1, 1, 41, 41] 41 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280250 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280250 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280250/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280250 Building REAL300000280251 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280251' /scratch/stefan/7769901/working/building/REAL300000280251 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280251 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280251/0 /scratch/stefan/7769901/working/building/REAL300000280251 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/359 `/scratch/stefan/7769901/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)SC=C1) `REAL300000280251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280251 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 32, 58, 58, 58, 58, 87, 87, 87, 58, 58, 1, 1, 1, 58, 58, 87, 87, 58, 58, 1, 1] 87 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280251 none N#CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 58, 58, 58, 1, 1, 2, 2, 1, 1, 58, 58] 87 rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 23, 24, 27, 28]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280251 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280251 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280251/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280251 Building REAL300000280252 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280252' /scratch/stefan/7769901/working/building/REAL300000280252 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280252 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280252/0 /scratch/stefan/7769901/working/building/REAL300000280252 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/360 `/scratch/stefan/7769901/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Cl)C=C2Cl)C=C1) `REAL300000280252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280252 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 139, 139, 201, 201, 196, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 139, 139, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 509 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280252 none O=C([O-])CC1=CC=C(NS(=O)(=O)C=CC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 129, 61, 9, 61, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 129, 9, 9, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 531 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280252 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280252 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280252/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280252 Building REAL300000280253 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280253' /scratch/stefan/7769901/working/building/REAL300000280253 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280253 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280253/0 /scratch/stefan/7769901/working/building/REAL300000280253 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/361 `/scratch/stefan/7769901/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280253 none CC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 37, 37, 37, 37, 54, 54, 54, 37, 37, 4, 4, 4, 3, 4, 4, 4, 1, 1, 37, 37, 54, 54, 37, 37] 54 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280253 none CC(C)N1N=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 37, 39, 37, 37, 37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 39, 39, 39, 39, 39, 39, 39, 37, 37, 1, 1, 2, 2, 1, 1] 54 rigid atoms, others: [32, 35, 36, 11, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280253 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280253 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280253/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280253 Building REAL300000280254 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280254' /scratch/stefan/7769901/working/building/REAL300000280254 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280254 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280254/0 /scratch/stefan/7769901/working/building/REAL300000280254 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/362 `/scratch/stefan/7769901/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300000280254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280254 none COC(=O)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 9, 9, 44, 44, 44, 28, 28, 1, 1, 1, 12, 12, 12, 1, 28, 28, 44, 44, 28, 28, 1, 2, 2, 2] 82 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 22, 23, 24, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280254 none COC(=O)C1=NC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 76, 28, 76, 28, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 28, 28, 28, 76, 76, 76, 28, 1, 1, 3, 3, 1, 1, 28, 28, 28, 28] 82 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280254 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280254/1 /scratch/stefan/7769901/working/building/REAL300000280254 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/363 `/scratch/stefan/7769901/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300000280254.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280254 none COC(=O)C1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 20, 15, 15, 34, 43, 43, 20, 20, 1, 1, 1, 13, 13, 13, 1, 9, 20, 20, 34, 34, 20, 20, 1, 2, 2, 2] 79 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 36, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280254 none COC(=O)C1=NC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 20, 77, 20, 20, 20, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 20, 20, 20, 77, 77, 77, 20, 6, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20] 79 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280254 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280254 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280254/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280254/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280254 Building REAL300000280255 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280255' /scratch/stefan/7769901/working/building/REAL300000280255 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280255 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280255/0 /scratch/stefan/7769901/working/building/REAL300000280255 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/364 `/scratch/stefan/7769901/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1) `REAL300000280255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 63, 63, 30, 10, 9, 10, 10, 9, 10, 10, 1, 1, 1, 3, 3, 1, 1, 10, 10, 63, 63, 63, 63, 63, 63, 30, 10, 10, 1, 1, 1, 1, 10, 10, 63, 63] 63 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 63, 63, 63, 63, 63, 22, 22, 1, 1, 2, 2, 1, 1, 9, 22, 22, 63, 63, 63, 63, 22, 22, 1, 1] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 22, 33, 22, 9, 22, 22, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 10, 15, 15, 10, 10, 1, 1, 22, 22, 22, 22, 22, 22, 5, 1, 1, 10, 10, 10, 10, 1, 1, 22, 22] 63 rigid atoms, others: [32, 37, 38, 9, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 164 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280255 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280255/1 /scratch/stefan/7769901/working/building/REAL300000280255 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/365 `/scratch/stefan/7769901/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1) `REAL300000280255.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 38, 51, 51, 28, 10, 2, 10, 10, 2, 10, 10, 1, 1, 1, 3, 3, 1, 1, 10, 10, 51, 51, 51, 51, 51, 51, 10, 10, 1, 1, 1, 1, 10, 10, 51, 51] 51 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 173 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 51, 51, 51, 51, 51, 20, 20, 1, 1, 2, 2, 1, 1, 20, 20, 51, 51, 51, 51, 20, 20, 1, 1] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 24, 25, 38, 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]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280255 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 29, 20, 9, 20, 20, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 10, 13, 13, 10, 10, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 10, 10, 10, 10, 1, 1, 20, 20] 51 rigid atoms, others: [36, 37, 9, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39]) total number of confs: 137 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280255 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280255 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280255/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280255/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280255 Building REAL300000280256 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280256' /scratch/stefan/7769901/working/building/REAL300000280256 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280256 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280256/0 /scratch/stefan/7769901/working/building/REAL300000280256 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/366 `/scratch/stefan/7769901/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280256 none N#CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 13, 13, 9, 9, 17, 17, 17, 13, 13, 1, 1, 1, 13, 13, 17, 17, 13, 13, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 24, 25, 26] set([32, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280256 none N#CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 13, 13, 13, 1, 1, 2, 2, 1, 1, 13] 17 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 29, 30, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280256 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280256 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280256/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280256 Building REAL300000280257 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280257' /scratch/stefan/7769901/working/building/REAL300000280257 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280257 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280257/0 /scratch/stefan/7769901/working/building/REAL300000280257 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/367 `/scratch/stefan/7769901/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CC2)C=C1) `REAL300000280257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280257 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 121, 64, 22, 64, 64, 22, 22, 22, 22, 7, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 22, 22, 7, 7, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280257 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 99, 99, 99, 99, 99, 163, 201, 201, 1, 1, 2, 2, 1, 1, 99, 99, 163, 163, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 37, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280257 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 125, 99, 99, 99, 99, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 5, 22, 22, 99, 99, 99, 99, 99, 99, 1, 1, 5, 5, 22, 22, 22, 22, 22, 99, 99] 201 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280257 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280257 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280257/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280257 Building REAL300000280258 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280258' /scratch/stefan/7769901/working/building/REAL300000280258 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280258 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280258/0 /scratch/stefan/7769901/working/building/REAL300000280258 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/368 `/scratch/stefan/7769901/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2=CC=CC=C2)C=C1) `REAL300000280258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280258 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 64, 61, 70, 70, 37, 17, 4, 17, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 4, 4, 1, 1, 1, 1, 1, 70, 70] 70 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37]) total number of confs: 211 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280258 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 2, 2, 1, 1, 70, 70, 70, 70, 70, 70, 70, 1, 1] 70 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280258 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=NN2C2=CC=CC=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 44, 41, 70, 70, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 70, 70, 70, 70, 70, 70, 1, 1, 4, 4, 4, 4, 4, 70, 70] 70 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 323 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280258 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280258 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280258/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280258 Building REAL300000280259 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280259' /scratch/stefan/7769901/working/building/REAL300000280259 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280259 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280259/0 /scratch/stefan/7769901/working/building/REAL300000280259 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/369 `/scratch/stefan/7769901/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280259 none COC1=NOC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 107, 143, 143, 123, 123, 185, 197, 197, 143, 143, 1, 3, 3, 3, 8, 8, 107, 143, 143, 185, 185, 143, 143, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 21] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280259 none COC1=NOC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [163, 143, 143, 143, 143, 57, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 143, 163, 163, 163, 57, 57, 6, 1, 1, 2, 2, 1, 1, 143] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280259 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280259 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280259/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280259 Building REAL300000280260 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280260' /scratch/stefan/7769901/working/building/REAL300000280260 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280260 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280260/0 /scratch/stefan/7769901/working/building/REAL300000280260 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/370 `/scratch/stefan/7769901/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=NN1C(C)C) `REAL300000280260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280260 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 29, 29, 45, 45, 45, 29, 29, 1, 1, 1, 1, 5, 5, 2, 2, 2, 29, 29, 45, 45, 29, 29, 1, 5, 6, 6, 6, 5, 5, 5] 45 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280260 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 29, 29, 29, 29, 35, 35, 29, 29, 29, 1, 1, 2, 2, 1, 1, 29, 35, 35, 35, 35, 35, 35, 35] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 121 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280260 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280260 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280260/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280260 Building REAL300000280261 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280261' /scratch/stefan/7769901/working/building/REAL300000280261 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280261 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280261/0 /scratch/stefan/7769901/working/building/REAL300000280261 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/371 `/scratch/stefan/7769901/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3(F)F)=C2)C=C1) `REAL300000280261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 20, 11, 20, 20, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 11, 73, 73, 73, 73, 73, 73, 45, 10, 11, 11, 1, 1, 1, 11, 73, 73] 73 rigid atoms, others: [33, 34, 35, 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, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 29, 29, 16, 29, 29, 73, 73, 73, 73, 29, 1, 1, 2, 2, 1, 1, 7, 29, 29, 16, 73, 73, 73, 29, 1, 1] 73 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 23, 24, 27, 28, 37] 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]) total number of confs: 264 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [35, 29, 35, 17, 17, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 11, 11, 11, 1, 29, 29] 73 rigid atoms, others: [32, 36, 9, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38]) total number of confs: 208 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280261 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280261/1 /scratch/stefan/7769901/working/building/REAL300000280261 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/372 `/scratch/stefan/7769901/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3(F)F)=C2)C=C1) `REAL300000280261.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 46, 19, 11, 19, 19, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 11, 69, 69, 69, 69, 69, 69, 10, 11, 11, 1, 1, 1, 11, 69, 69] 69 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 30, 30, 17, 30, 30, 69, 69, 69, 69, 30, 1, 1, 2, 2, 1, 1, 30, 30, 17, 69, 69, 69, 30, 1, 1] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 255 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280261 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C3CC3(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [38, 30, 38, 17, 17, 30, 30, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 30, 30, 30, 30, 30, 30, 1, 1, 1, 11, 11, 11, 1, 30, 30] 69 rigid atoms, others: [35, 9, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37]) total number of confs: 216 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280261 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280261 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280261/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280261/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280261 Building REAL300000280262 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280262' /scratch/stefan/7769901/working/building/REAL300000280262 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280262 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280262/0 /scratch/stefan/7769901/working/building/REAL300000280262 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/373 `/scratch/stefan/7769901/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)F)=C2)C=C1) `REAL300000280262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280262 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 28, 28, 28, 28, 28, 46, 46, 28, 1, 1, 2, 2, 1, 1, 28, 28, 46, 28, 1, 1] 46 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280262 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CN=CC(C(F)F)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [30, 28, 30, 15, 15, 28, 28, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 1, 28, 28, 28, 28, 28, 28, 1, 1, 11, 1, 28, 28] 46 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 29, 31, 32]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280262 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280262/1 /scratch/stefan/7769901/working/building/REAL300000280262 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/374 `/scratch/stefan/7769901/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)F)=C2)C=C1) `REAL300000280262.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280262 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 28, 28, 28, 28, 28, 46, 46, 28, 1, 1, 2, 2, 1, 1, 7, 28, 28, 46, 28, 1, 1] 46 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280262 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CN=CC(C(F)F)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 28, 16, 16, 28, 28, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 1, 28, 28, 28, 28, 28, 28, 9, 1, 1, 12, 1, 28, 28] 46 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 32, 33]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280262 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280262 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280262/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280262/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280262 Building REAL300000280263 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280263' /scratch/stefan/7769901/working/building/REAL300000280263 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280263 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280263/0 /scratch/stefan/7769901/working/building/REAL300000280263 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/375 `/scratch/stefan/7769901/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(S(=O)(=O)F)=CS2)C=C1) `REAL300000280263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280263 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(S(=O)(=O)F)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 14, 11, 11, 15, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 75, 75, 75, 100, 100, 100, 75, 75, 1, 1, 1, 1, 1, 1, 75, 75, 1, 1] 100 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280263 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(S(=O)(=O)F)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 14, 11, 11, 15, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 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: [75, 75, 75, 75, 58, 75, 75, 25, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 75, 75, 75, 75, 75, 75, 1, 1, 75, 75] 100 rigid atoms, others: [9, 12, 13, 14, 15, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280263 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280263 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280263/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280263 Building REAL300000280264 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280264' /scratch/stefan/7769901/working/building/REAL300000280264 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280264 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280264/0 /scratch/stefan/7769901/working/building/REAL300000280264 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/376 `/scratch/stefan/7769901/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1) `REAL300000280264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280264 none CC(C)C1CC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 7, 37, 37, 37, 81, 136, 136, 106, 112, 167, 167, 167, 136, 136, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 81, 136, 136, 167, 167, 136, 136, 1, 1] 167 rigid atoms, others: [32, 1, 3, 4, 5, 6, 42, 43, 21, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 778 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280264 none CC(C)C1CC(CS(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [140, 136, 140, 136, 136, 84, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 136, 140, 140, 140, 140, 140, 140, 140, 136, 136, 136, 136, 84, 84, 7, 1, 1, 2, 2, 1, 1, 136, 136] 167 rigid atoms, others: [36, 37, 40, 41, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43]) total number of confs: 537 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280264 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280264 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280264/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280264 Building REAL300000280265 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280265' /scratch/stefan/7769901/working/building/REAL300000280265 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280265 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280265/0 /scratch/stefan/7769901/working/building/REAL300000280265 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/377 `/scratch/stefan/7769901/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1OC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280265 none CC1=CC=CC=C1OC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 65, 22, 22, 22, 22, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 22, 22, 147, 147, 147, 147, 147, 147, 147, 22, 22, 6, 1, 1, 2, 2, 1, 1, 22, 22] 186 rigid atoms, others: [38, 39, 42, 43, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45]) total number of confs: 270 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280265 none CC1=CC=CC=C1OC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 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, 8, 14, 14, 8, 14, 27, 27, 27, 89, 147, 147, 122, 146, 186, 186, 186, 147, 147, 14, 14, 2, 2, 2, 1, 1, 1, 1, 14, 14, 89, 147, 147, 186, 186, 147, 147, 14, 14] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 31] set([8, 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, 43, 44, 45]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280265 none CC1=CC=CC=C1OC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 17, 22, 34, 40, 40, 22, 22, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1, 1, 9, 22, 22, 34, 34, 22, 22, 1, 1] 186 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280265 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280265 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280265/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280265 Building REAL300000280266 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280266' /scratch/stefan/7769901/working/building/REAL300000280266 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280266 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280266/0 /scratch/stefan/7769901/working/building/REAL300000280266 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/378 `/scratch/stefan/7769901/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3(F)F)C=C2)C=C1) `REAL300000280266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 30, 11, 5, 11, 11, 1, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 46, 46, 46, 46, 46, 46, 30, 10, 10, 1, 1, 1, 10, 10, 46, 46] 46 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 46, 46, 46, 46, 17, 17, 1, 1, 2, 2, 1, 1, 7, 17, 17, 46, 46, 46, 17, 17, 1, 1] 46 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 23, 24, 27, 28, 37] 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]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 14, 9, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 10, 10, 10, 1, 1, 17, 17] 46 rigid atoms, others: [35, 36, 9, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 123 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280266 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280266/1 /scratch/stefan/7769901/working/building/REAL300000280266 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/379 `/scratch/stefan/7769901/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3(F)F)C=C2)C=C1) `REAL300000280266.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 48, 49, 49, 32, 11, 10, 11, 11, 1, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 49, 49, 49, 49, 49, 49, 10, 10, 1, 1, 1, 10, 10, 49, 49] 49 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 49, 49, 49, 49, 18, 18, 1, 1, 2, 2, 1, 1, 18, 18, 49, 49, 49, 18, 18, 1, 1] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280266 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 18, 22, 17, 9, 18, 18, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 18, 18, 18, 18, 18, 18, 1, 1, 10, 10, 10, 1, 1, 18, 18] 49 rigid atoms, others: [34, 35, 9, 12, 13, 14, 15, 16, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37]) total number of confs: 110 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280266 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280266 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280266/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280266/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280266 Building REAL300000280267 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280267' /scratch/stefan/7769901/working/building/REAL300000280267 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280267 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280267/0 /scratch/stefan/7769901/working/building/REAL300000280267 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/380 `/scratch/stefan/7769901/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1) `REAL300000280267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280267 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 1, 1, 59, 59, 59, 59, 59, 1, 1] 59 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280267 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 51, 49, 59, 59, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 59, 59] 59 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 33, 22, 23, 24, 25, 26, 27]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280267 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280267/1 /scratch/stefan/7769901/working/building/REAL300000280267 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/381 `/scratch/stefan/7769901/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1) `REAL300000280267.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280267 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 1, 1, 11, 59, 59, 59, 59, 59, 1, 1] 59 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280267 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 59, 59, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 25, 1, 1, 1, 1, 1, 59, 59] 59 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 35, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280267 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280267 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280267/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280267/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280267 Building REAL300000280268 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280268' /scratch/stefan/7769901/working/building/REAL300000280268 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280268 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280268/0 /scratch/stefan/7769901/working/building/REAL300000280268 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/382 `/scratch/stefan/7769901/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=C2)C=C1) `REAL300000280268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280268 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 2, 2, 1, 1, 8, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280268 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 26, 26, 8, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280268 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280268/1 /scratch/stefan/7769901/working/building/REAL300000280268 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/383 `/scratch/stefan/7769901/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=C2)C=C1) `REAL300000280268.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280268 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 24, 25, 38, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280268 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 10, 10, 19, 19, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280268 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280268 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280268/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280268/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280268 Building REAL300000280269 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280269' /scratch/stefan/7769901/working/building/REAL300000280269 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280269 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280269/0 /scratch/stefan/7769901/working/building/REAL300000280269 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/384 `/scratch/stefan/7769901/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(O)=C2)C=C1) `REAL300000280269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280269 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(O)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 7, 23, 23, 23, 46, 23, 1, 1] 46 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 19, 20, 23, 24, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280269 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC(O)=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 2, 1, 23, 23] 46 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 32, 29, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280269 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280269/1 /scratch/stefan/7769901/working/building/REAL300000280269 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/385 `/scratch/stefan/7769901/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(O)=C2)C=C1) `REAL300000280269.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280269 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(O)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 1, 22, 22, 22, 44, 22, 1, 1] 44 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280269 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC(O)=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 22, 22, 17, 17, 22, 22, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 1, 22, 22] 44 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 28, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280269 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280269 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280269/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280269/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280269 Building REAL300000280270 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280270' /scratch/stefan/7769901/working/building/REAL300000280270 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280270 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280270/0 /scratch/stefan/7769901/working/building/REAL300000280270 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/386 `/scratch/stefan/7769901/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1) `REAL300000280270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280270 none COC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 6, 35, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 25, 25, 19, 19, 41, 49, 49, 25, 25, 35, 35, 35, 6, 6, 1, 1, 1, 1, 11, 25, 25, 41, 41, 25, 25] 169 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]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280270 none COC(=O)CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 67, 121, 25, 25, 25, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 121, 121, 121, 67, 67, 25, 25, 25, 25, 6, 1, 1, 3, 3, 1, 1] 169 rigid atoms, others: [35, 36, 39, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280270 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280270/1 /scratch/stefan/7769901/working/building/REAL300000280270 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/387 `/scratch/stefan/7769901/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280270.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280270 none COC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 33, 33, 24, 24, 55, 60, 60, 33, 33, 27, 27, 27, 6, 6, 1, 1, 1, 1, 33, 33, 55, 55, 33, 33] 171 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]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280270 none COC(=O)CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [141, 141, 79, 141, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 141, 141, 141, 79, 79, 33, 33, 33, 33, 1, 1, 2, 2, 1, 1] 171 rigid atoms, others: [34, 35, 38, 39, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280270 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280270 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280270/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280270/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280270 Building REAL300000280271 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280271' /scratch/stefan/7769901/working/building/REAL300000280271 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280271 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280271/0 /scratch/stefan/7769901/working/building/REAL300000280271 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/388 `/scratch/stefan/7769901/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(F)F)=CC=C2F)C=C1) `REAL300000280271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280271 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(F)F)=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 69, 69, 69, 79, 79, 29, 69, 69, 69, 1, 1, 1, 1, 1, 1, 69, 79, 41, 69, 1, 1] 79 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 22, 23, 24, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280271 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC(C(F)F)=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [75, 69, 75, 69, 36, 69, 69, 19, 7, 1, 7, 7, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 1, 12, 1, 1, 69, 69] 79 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 29, 32, 33]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280271 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280271 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280271/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280271 Building REAL300000280272 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280272' /scratch/stefan/7769901/working/building/REAL300000280272 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280272 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280272/0 /scratch/stefan/7769901/working/building/REAL300000280272 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/389 `/scratch/stefan/7769901/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=NN(C3CC3(F)F)C=C2)C=C1) `REAL300000280272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280272 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=NN(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 174, 184, 184, 124, 57, 13, 57, 57, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 184, 184, 184, 184, 184, 184, 1, 1, 1, 13, 13, 184, 184] 184 rigid atoms, others: [14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280272 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=NN(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 94, 94, 94, 184, 184, 184, 184, 94, 94, 1, 1, 1, 1, 1, 1, 184, 184, 184, 94, 94, 1, 1] 184 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280272 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=NN(C3CC3(F)F)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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [107, 94, 107, 94, 43, 94, 94, 25, 6, 1, 6, 6, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 94, 94, 94, 94, 94, 94, 13, 13, 13, 1, 1, 94, 94] 184 rigid atoms, others: [32, 9, 12, 13, 14, 15, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280272 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280272 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280272/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280272 Building REAL300000280273 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280273' /scratch/stefan/7769901/working/building/REAL300000280273 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280273 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280273/0 /scratch/stefan/7769901/working/building/REAL300000280273 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/390 `/scratch/stefan/7769901/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1) `REAL300000280273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 53, 53, 64, 64, 28, 14, 6, 14, 14, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 28, 6, 1, 6, 6, 1, 1, 1, 64, 64] 64 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 254 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 1, 1, 1, 1, 1, 1, 11, 28, 28, 28, 42, 42, 42, 42, 42, 42, 64, 64, 64, 64, 1, 1, 2, 2, 1, 1, 11, 42, 42, 42, 42, 64, 64, 64, 1, 1] 64 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 23, 24, 27, 28, 37] 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]) total number of confs: 222 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 43, 24, 24, 42, 42, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 42, 42, 42, 42, 42, 42, 13, 1, 1, 1, 1, 6, 6, 6, 42, 42] 64 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280273 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280273/1 /scratch/stefan/7769901/working/building/REAL300000280273 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/391 `/scratch/stefan/7769901/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1) `REAL300000280273.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 36, 16, 4, 16, 16, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 4, 4, 4, 4, 1, 1, 1, 77, 77] 77 rigid atoms, others: [33, 34, 35, 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, 36, 37]) total number of confs: 153 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 65, 65, 30, 65, 65, 65, 77, 77, 77, 77, 1, 1, 2, 2, 1, 1, 65, 65, 30, 65, 77, 77, 77, 1, 1] 77 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 264 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280273 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [67, 65, 67, 65, 65, 65, 65, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 4, 4, 4, 65, 65] 77 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 121 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280273 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280273 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280273/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280273/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280273 Building REAL300000280274 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280274' /scratch/stefan/7769901/working/building/REAL300000280274 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280274 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280274/0 /scratch/stefan/7769901/working/building/REAL300000280274 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/392 `/scratch/stefan/7769901/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl) `REAL300000280274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280274 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 13, 17, 21, 21, 21, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 21, 21, 17, 17] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280274 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1] 21 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280274 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280274/1 /scratch/stefan/7769901/working/building/REAL300000280274 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/393 `/scratch/stefan/7769901/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl) `REAL300000280274.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280274 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 15, 15, 12, 15, 17, 17, 17, 15, 15, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 15, 15, 17, 17, 15, 15] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280274 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 15, 15, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 3, 3, 1, 1] 17 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280274 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280274 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280274/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280274/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280274 Building REAL300000280275 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280275' /scratch/stefan/7769901/working/building/REAL300000280275 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280275 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280275/0 /scratch/stefan/7769901/working/building/REAL300000280275 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/394 `/scratch/stefan/7769901/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1) `REAL300000280275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280275 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 17, 17, 11, 13, 26, 26, 26, 26, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 1, 1] 26 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280275 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 17, 11, 17, 17, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 12, 16, 16, 16, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 26 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280275 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280275/1 /scratch/stefan/7769901/working/building/REAL300000280275 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/395 `/scratch/stefan/7769901/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1) `REAL300000280275.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280275 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 19, 19, 11, 13, 31, 31, 31, 31, 19, 19, 19, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 1, 1] 31 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280275 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 19, 25, 19, 11, 19, 19, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 11, 15, 15, 15, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 19, 19] 31 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280275 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280275 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280275/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280275/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280275 Building REAL300000280276 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280276' /scratch/stefan/7769901/working/building/REAL300000280276 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280276 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280276/0 /scratch/stefan/7769901/working/building/REAL300000280276 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/396 `/scratch/stefan/7769901/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)N(C3=CC=CC=C3)N=C2)C=C1) `REAL300000280276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280276 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)N(C3=CC=CC=C3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 49, 17, 4, 17, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 4, 76, 76] 76 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 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, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280276 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)N(C3=CC=CC=C3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 2, 2, 1, 1, 76, 76, 76, 76, 76, 76, 1, 1] 76 rigid atoms, others: [3, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280276 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C(F)N(C3=CC=CC=C3)N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 76, 76, 76, 76, 76, 76, 4, 4, 1, 4, 4, 1, 76, 76] 76 rigid atoms, others: [35, 9, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280276 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280276 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280276/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280276 Building REAL300000280277 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280277' /scratch/stefan/7769901/working/building/REAL300000280277 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280277 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280277/0 /scratch/stefan/7769901/working/building/REAL300000280277 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/397 `/scratch/stefan/7769901/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1) `REAL300000280277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280277 none COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 33, 33, 25, 33, 62, 62, 62, 33, 33, 1, 1, 5, 5, 1, 3, 3, 3, 1, 1, 11, 33, 33, 62, 62, 33, 33, 5, 1] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 24, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280277 none COC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [54, 19, 19, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 33, 33, 53, 53, 33, 54, 54, 54, 33, 33, 6, 1, 1, 3, 3, 1, 1, 53, 33] 96 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280277 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280277/1 /scratch/stefan/7769901/working/building/REAL300000280277 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/398 `/scratch/stefan/7769901/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1) `REAL300000280277.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280277 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 20, 31, 53, 60, 60, 31, 31, 1, 1, 5, 5, 1, 3, 3, 3, 1, 1, 31, 31, 53, 53, 31, 31, 5, 1] 78 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 24, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280277 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [40, 23, 17, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 31, 31, 49, 49, 31, 40, 40, 40, 31, 31, 1, 1, 3, 3, 1, 1, 49, 31] 78 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280277 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280277 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280277/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280277/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280277 Building REAL300000280278 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280278' /scratch/stefan/7769901/working/building/REAL300000280278 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280278 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280278/0 /scratch/stefan/7769901/working/building/REAL300000280278 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/399 `/scratch/stefan/7769901/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC) `REAL300000280278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280278 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 12, 12, 26, 41, 41, 15, 15, 1, 1, 1, 12, 12, 12, 28, 28, 28, 27, 27, 1, 1, 9, 15, 15, 26, 26, 15, 15, 1, 12, 12, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 21, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280278 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 54, 15, 15, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 15, 15, 15, 87, 87, 87, 122, 122, 122, 122, 122, 15, 15, 4, 1, 1, 2, 2, 1, 1, 15, 87, 87, 87] 201 rigid atoms, others: [35, 36, 39, 40, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280278 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280278/1 /scratch/stefan/7769901/working/building/REAL300000280278 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/400 `/scratch/stefan/7769901/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC) `REAL300000280278.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280278 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 13, 27, 47, 47, 17, 17, 1, 1, 1, 12, 12, 12, 28, 28, 28, 27, 27, 1, 1, 17, 17, 27, 27, 17, 17, 1, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280278 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 64, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 17, 17, 102, 102, 102, 120, 120, 120, 120, 120, 17, 17, 1, 1, 2, 2, 1, 1, 17, 102, 102, 102] 201 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280278 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280278 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280278/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280278/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280278 Building REAL300000280279 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280279' /scratch/stefan/7769901/working/building/REAL300000280279 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280279 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280279/0 /scratch/stefan/7769901/working/building/REAL300000280279 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/401 `/scratch/stefan/7769901/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1) `REAL300000280279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280279 none COC(=O)C1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 14, 13, 24, 24, 24, 18, 18, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 9, 18, 18, 24, 24, 18, 18, 1, 1, 1] 55 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 44, 34, 24, 25, 26, 42, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280279 none COC(=O)C1CC2=CC=C(S(=O)(=O)NC3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 18, 41, 18, 18, 18, 18, 18, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 18, 18, 18, 41, 41, 41, 18, 18, 18, 18, 18, 6, 1, 1, 2, 2, 1, 1, 18, 18, 18] 55 rigid atoms, others: [36, 37, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280279 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280279/1 /scratch/stefan/7769901/working/building/REAL300000280279 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/402 `/scratch/stefan/7769901/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1) `REAL300000280279.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280279 none COC(=O)C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 16, 16, 28, 28, 28, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 27, 27, 28, 28, 27, 27, 1, 1, 1] 68 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 34, 41, 24, 25, 26, 42, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280279 none COC(=O)C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(CC(=O)[O-])C=C3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 67, 27, 67, 27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 27, 27, 27, 67, 67, 67, 27, 27, 27, 27, 27, 1, 1, 2, 2, 1, 1, 27, 27, 27] 68 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280279 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280279 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280279/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280279/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280279 Building REAL300000280280 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280280' /scratch/stefan/7769901/working/building/REAL300000280280 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280280 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280280/0 /scratch/stefan/7769901/working/building/REAL300000280280 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/403 `/scratch/stefan/7769901/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280280 none COC(=O)C1=CC=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 33, 33, 33, 33, 43, 45, 45, 33, 33, 5, 5, 5, 1, 1, 1, 33, 33, 43, 43, 33, 33] 69 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280280 none COC(=O)C1=CC=NC=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [53, 53, 33, 53, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 53, 53, 53, 33, 33, 33, 1, 1, 2, 2, 1, 1] 69 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280280 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280280 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280280/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280280 Building REAL300000280281 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280281' /scratch/stefan/7769901/working/building/REAL300000280281 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280281 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280281/0 /scratch/stefan/7769901/working/building/REAL300000280281 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/404 `/scratch/stefan/7769901/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280281 none COC1=NC=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 25, 50, 50, 36, 50, 58, 58, 58, 50, 50, 4, 4, 4, 1, 1, 50, 50, 58, 58, 50, 50] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280281 none COC1=NC=C(C(F)(F)F)C=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [54, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 54, 54, 54, 50, 50, 1, 1, 2, 2, 1, 1] 58 rigid atoms, others: [32, 35, 36, 15, 16, 17, 18, 19, 20, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280281 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280281 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280281/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280281 Building REAL300000280282 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280282' /scratch/stefan/7769901/working/building/REAL300000280282 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280282 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280282/0 /scratch/stefan/7769901/working/building/REAL300000280282 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/405 `/scratch/stefan/7769901/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280282 none COC(=O)C1=CC=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 46, 46, 30, 31, 62, 62, 62, 46, 46, 6, 6, 6, 1, 1, 1, 46, 46, 62, 62, 46, 46] 97 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280282 none COC(=O)C1=CC=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 76, 46, 76, 46, 46, 28, 46, 46, 46, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 76, 76, 76, 46, 46, 46, 1, 1, 2, 2, 1, 1] 97 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280282 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280282 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280282/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280282 Building REAL300000280283 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280283' /scratch/stefan/7769901/working/building/REAL300000280283 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280283 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280283/0 /scratch/stefan/7769901/working/building/REAL300000280283 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/406 `/scratch/stefan/7769901/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12) `REAL300000280283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280283 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 21, 39, 39, 30, 30, 41, 41, 41, 39, 39, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 41, 41, 39, 39, 1, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 23, 24, 36, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280283 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 2, 2, 1, 1, 39, 39, 39] 41 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280283 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280283/1 /scratch/stefan/7769901/working/building/REAL300000280283 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/407 `/scratch/stefan/7769901/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12) `REAL300000280283.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280283 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 19, 31, 31, 25, 25, 35, 35, 35, 31, 31, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 31, 31, 35, 35, 31, 31, 1, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280283 none CC1=CC=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 2, 2, 1, 1, 31, 31, 31] 35 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280283 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280283 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280283/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280283/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280283 Building REAL300000280284 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280284' /scratch/stefan/7769901/working/building/REAL300000280284 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280284 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280284/0 /scratch/stefan/7769901/working/building/REAL300000280284 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/408 `/scratch/stefan/7769901/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1) `REAL300000280284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280284 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 21, 43, 43, 31, 31, 55, 55, 55, 43, 43, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 55, 55, 43, 43, 1] 63 rigid atoms, others: [1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 23] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280284 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [58, 43, 43, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 43, 43, 43, 43, 43, 43, 58, 58, 58, 58, 58, 1, 1, 2, 2, 1, 1, 43] 63 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 185 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280284 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280284/1 /scratch/stefan/7769901/working/building/REAL300000280284 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/409 `/scratch/stefan/7769901/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1) `REAL300000280284.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280284 none CCC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 3, 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: [6, 1, 1, 1, 1, 5, 5, 5, 15, 32, 32, 23, 23, 44, 44, 44, 32, 32, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 15, 32, 32, 44, 44, 32, 32, 1] 48 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 36] set([0, 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280284 none CCC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 3, 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: [46, 32, 32, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 32, 32, 32, 32, 32, 32, 46, 46, 46, 46, 46, 6, 1, 1, 2, 2, 1, 1, 32] 48 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280284 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280284 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280284/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280284/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280284 Building REAL300000280285 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280285' /scratch/stefan/7769901/working/building/REAL300000280285 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280285 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280285/0 /scratch/stefan/7769901/working/building/REAL300000280285 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/410 `/scratch/stefan/7769901/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280285 none CC1=CC=C(OC(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 17, 17, 1, 1, 7, 7, 7, 23, 51, 51, 35, 35, 93, 105, 105, 51, 51, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 51, 51, 93, 93, 51, 51, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 43, 24, 28, 29] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 501 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280285 none CC1=CC=C(OC(C)C)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 51, 27, 51, 51, 51, 111, 136, 136, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 51, 51, 51, 51, 51, 51, 136, 136, 136, 136, 136, 136, 136, 1, 1, 2, 2, 1, 1, 51] 159 rigid atoms, others: [37, 38, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43]) total number of confs: 457 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280285 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280285/1 /scratch/stefan/7769901/working/building/REAL300000280285 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/411 `/scratch/stefan/7769901/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280285 none CC1=CC=C(OC(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 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, 8, 19, 19, 1, 1, 7, 7, 7, 25, 62, 62, 43, 43, 105, 127, 127, 62, 62, 1, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 19, 25, 62, 62, 105, 105, 62, 62, 1] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 44, 24, 28, 29] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 618 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280285 none CC1=CC=C(OC(C)C)C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 28, 62, 62, 62, 131, 169, 169, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 62, 62, 62, 62, 62, 62, 169, 169, 169, 169, 169, 169, 169, 6, 1, 1, 2, 2, 1, 1, 62] 188 rigid atoms, others: [38, 39, 42, 43, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44]) total number of confs: 607 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280285 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280285 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280285/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280285/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280285 Building REAL300000280286 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280286' /scratch/stefan/7769901/working/building/REAL300000280286 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280286 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280286/0 /scratch/stefan/7769901/working/building/REAL300000280286 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/412 `/scratch/stefan/7769901/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1) `REAL300000280286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280286 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 12, 17, 25, 25, 25, 17, 17, 1, 1, 1, 1, 2, 2, 2, 17, 17, 25, 25, 17, 17, 1] 25 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280286 none CC1=C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 17] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280286 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280286/1 /scratch/stefan/7769901/working/building/REAL300000280286 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/413 `/scratch/stefan/7769901/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1) `REAL300000280286.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280286 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 19, 19, 16, 19, 25, 25, 25, 19, 19, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 25, 25, 19, 19, 1] 25 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280286 none CC1=C(S(=O)(=O)NC2=CC=C(CC(=O)[O-])C=C2)C=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [19, 19, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 3, 3, 1, 1, 19] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280286 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280286 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280286/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280286/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280286 Building REAL300000280287 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280287' /scratch/stefan/7769901/working/building/REAL300000280287 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280287 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280287/0 /scratch/stefan/7769901/working/building/REAL300000280287 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/414 `/scratch/stefan/7769901/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1) `REAL300000280287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280287 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 2, 2, 1, 1, 61, 61, 61, 61, 61, 1, 1] 61 rigid atoms, others: [3, 4, 5, 6, 7, 8, 37, 25, 26, 29, 30, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280287 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 61, 61] 61 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280287 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280287/1 /scratch/stefan/7769901/working/building/REAL300000280287 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/415 `/scratch/stefan/7769901/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1) `REAL300000280287.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280287 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 2, 2, 1, 1, 11, 62, 62, 62, 62, 62, 1, 1] 62 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 38, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280287 none O=C([O-])CC1=CC=C(NS(=O)(=O)C2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 49, 49, 62, 62, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 62, 62, 62, 62, 62, 62, 25, 1, 1, 1, 1, 1, 62, 62] 62 rigid atoms, others: [32, 33, 34, 35, 36, 9, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280287 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280287 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280287/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280287/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280287 Building REAL300000280288 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280288' /scratch/stefan/7769901/working/building/REAL300000280288 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280288 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280288/0 /scratch/stefan/7769901/working/building/REAL300000280288 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/416 `/scratch/stefan/7769901/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3CCCCN3N=C2)C=C1) `REAL300000280288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280288 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3CCCCN3N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1] 40 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 37, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280288 none O=C([O-])CC1=CC=C([N-]S(=O)(=O)C2=C3CCCCN3N=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', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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: [11, 1, 11, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 34, 40, 40, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 40 rigid atoms, others: [32, 33, 34, 35, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280288 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280288 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280288/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280288 Building REAL300000280289 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280289' /scratch/stefan/7769901/working/building/REAL300000280289 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280289 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280289/0 /scratch/stefan/7769901/working/building/REAL300000280289 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/417 `/scratch/stefan/7769901/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000280289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280289 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 43, 43, 37, 37, 47, 47, 47, 43, 43, 1, 2, 2, 2, 1, 1, 43, 43, 47, 47, 43, 43, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280289 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1, 43] 47 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280289 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280289 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280289/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280289 Building REAL300000280290 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280290' /scratch/stefan/7769901/working/building/REAL300000280290 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280290 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280290/0 /scratch/stefan/7769901/working/building/REAL300000280290 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/418 `/scratch/stefan/7769901/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000280290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280290 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 47, 47, 27, 58, 58, 58, 58, 58, 36, 36, 8, 1, 1, 1, 1, 27, 27, 27] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280290 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 64, 64, 27, 64, 27, 27, 27, 27, 27, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 145, 145, 64, 27, 27, 27, 27, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 880 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280290 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280290 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280290/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280290 Building REAL300000280291 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280291' /scratch/stefan/7769901/working/building/REAL300000280291 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280291 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280291/0 /scratch/stefan/7769901/working/building/REAL300000280291 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/419 `/scratch/stefan/7769901/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300000280291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280291 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 36, 36, 10, 1, 1, 1, 1, 15, 15, 15, 15] 133 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280291 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 68, 68, 15, 68, 15, 15, 15, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 68, 15, 15, 15, 15, 1, 1, 1, 1] 133 rigid atoms, others: [37, 38, 39, 40, 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]) total number of confs: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280291 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280291 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280291/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280291 Building REAL300000280292 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280292' /scratch/stefan/7769901/working/building/REAL300000280292 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280292 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280292/0 /scratch/stefan/7769901/working/building/REAL300000280292 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/420 `/scratch/stefan/7769901/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300000280292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280292 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 44, 44, 44, 44, 44, 30, 30, 8, 1, 1, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280292 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 95, 95, 29, 95, 29, 29, 23, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 95, 29, 29, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280292 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280292 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280292/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280292 Building REAL300000280293 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280293' /scratch/stefan/7769901/working/building/REAL300000280293 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280293 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280293/0 /scratch/stefan/7769901/working/building/REAL300000280293 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/421 `/scratch/stefan/7769901/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC) `REAL300000280293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280293 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 49, 49, 49, 49, 49, 49, 49, 49, 49, 68, 47, 47, 47, 47, 47, 28, 28, 6, 1, 1, 1, 1, 49, 49, 49, 68, 68, 68] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280293 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 189, 90, 90, 49, 90, 49, 49, 49, 49, 49, 23, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 201, 201, 201, 201, 201, 189, 189, 90, 49, 49, 49, 49, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [39, 40, 41, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280293 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280293 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280293/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280293 Building REAL300000280294 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280294' /scratch/stefan/7769901/working/building/REAL300000280294 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280294 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280294/0 /scratch/stefan/7769901/working/building/REAL300000280294 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/422 `/scratch/stefan/7769901/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000280294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280294 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 49, 48, 84, 84, 13, 13, 65, 65, 65, 65, 65, 40, 40, 8, 1, 1, 1, 1, 13, 13, 49, 49, 13, 13] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280294 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 89, 31, 31, 13, 31, 13, 13, 12, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 131, 131, 131, 131, 131, 89, 89, 31, 13, 13, 13, 13, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [39, 40, 44, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 671 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280294 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280294 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280294/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280294 Building REAL300000280295 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280295' /scratch/stefan/7769901/working/building/REAL300000280295 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280295 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280295/0 /scratch/stefan/7769901/working/building/REAL300000280295 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/423 `/scratch/stefan/7769901/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1) `REAL300000280295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280295 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 61, 61, 61, 61, 61, 45, 45, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280295 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 97, 29, 97, 29, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 97, 29, 29, 29, 29, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [38, 39, 43, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280295 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280295 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280295/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280295 Building REAL300000280296 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280296' /scratch/stefan/7769901/working/building/REAL300000280296 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280296 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280296/0 /scratch/stefan/7769901/working/building/REAL300000280296 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/424 `/scratch/stefan/7769901/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl) `REAL300000280296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280296 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 49, 49, 49, 49, 49, 36, 36, 8, 1, 1, 1, 1, 26, 26, 26] 140 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280296 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 68, 68, 26, 68, 26, 26, 26, 26, 26, 12, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 68, 26, 26, 26, 26, 1, 1, 1] 140 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280296 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280296 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280296/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280296 Building REAL300000280297 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280297' /scratch/stefan/7769901/working/building/REAL300000280297 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280297 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280297/0 /scratch/stefan/7769901/working/building/REAL300000280297 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/425 `/scratch/stefan/7769901/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000280297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280297 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 37, 37, 29, 60, 60, 60, 60, 60, 46, 46, 10, 1, 1, 1, 1, 29, 29, 29] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280297 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 91, 91, 29, 91, 29, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 199, 199, 91, 29, 29, 29, 29, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280297 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280297 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280297/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280297 Building REAL300000280298 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280298' /scratch/stefan/7769901/working/building/REAL300000280298 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280298 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280298/0 /scratch/stefan/7769901/working/building/REAL300000280298 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/426 `/scratch/stefan/7769901/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C) `REAL300000280298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280298 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 59, 59, 59, 59, 59, 39, 39, 9, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42] 187 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 375 number of broken/clashed sets: 186 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280298 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 90, 42, 90, 42, 42, 42, 42, 42, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 187, 90, 42, 42, 42, 42, 1, 1, 2, 2, 2, 2, 2, 2] 187 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 681 number of broken/clashed sets: 186 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280298 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280298 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280298/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280298 Building REAL300000280299 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280299' /scratch/stefan/7769901/working/building/REAL300000280299 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280299 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280299/0 /scratch/stefan/7769901/working/building/REAL300000280299 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/427 `/scratch/stefan/7769901/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000280299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280299 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 35, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 55, 55, 55, 55, 55, 55, 55, 55, 55, 57, 57, 57, 57, 57, 35, 35, 8, 1, 1, 1, 1, 55, 55, 55] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280299 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 106, 55, 106, 55, 55, 55, 55, 55, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 106, 55, 55, 55, 55, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280299 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280299 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280299/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280299 Building REAL300000280300 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280300' /scratch/stefan/7769901/working/building/REAL300000280300 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280300 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280300/0 /scratch/stefan/7769901/working/building/REAL300000280300 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/428 `/scratch/stefan/7769901/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000280300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280300 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 23, 23, 44, 44, 11, 11, 32, 32, 32, 32, 32, 18, 18, 6, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 11, 11] 121 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280300 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 50, 21, 21, 11, 21, 11, 11, 10, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 1, 1, 67, 67, 67, 67, 67, 50, 50, 21, 11, 11, 11, 11, 1, 1, 4, 4, 4, 4, 1, 1] 121 rigid atoms, others: [45, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280300 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280300 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280300/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280300 Building REAL300000280301 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280301' /scratch/stefan/7769901/working/building/REAL300000280301 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280301 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280301/0 /scratch/stefan/7769901/working/building/REAL300000280301 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/429 `/scratch/stefan/7769901/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1) `REAL300000280301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280301 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 57, 57, 57, 57, 57, 57, 57, 54, 54, 54, 54, 54, 32, 32, 8, 1, 1, 1, 1, 57, 57] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 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: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280301 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 110, 110, 57, 110, 57, 57, 57, 57, 57, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 110, 57, 57, 57, 57, 1, 1] 201 rigid atoms, others: [36, 37, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280301 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280301 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280301/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280301 Building REAL300000280302 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280302' /scratch/stefan/7769901/working/building/REAL300000280302 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280302 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280302/0 /scratch/stefan/7769901/working/building/REAL300000280302 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/430 `/scratch/stefan/7769901/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000280302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280302 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 38, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 57, 57, 57, 57, 57, 38, 38, 8, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 183 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280302 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 85, 85, 41, 85, 41, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 85, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 183 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280302 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280302 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280302/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280302 Building REAL300000280303 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280303' /scratch/stefan/7769901/working/building/REAL300000280303 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280303 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280303/0 /scratch/stefan/7769901/working/building/REAL300000280303 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/431 `/scratch/stefan/7769901/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000280303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280303 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 55, 67, 89, 89, 11, 11, 48, 48, 48, 48, 48, 30, 30, 8, 1, 1, 1, 1, 11, 11, 67, 67, 11, 11] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280303 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 59, 21, 21, 11, 21, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 23, 23, 1, 1, 91, 91, 91, 91, 91, 59, 59, 21, 11, 11, 11, 11, 1, 1, 10, 10, 1, 1] 201 rigid atoms, others: [39, 40, 44, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280303 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280303 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280303/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280303 Building REAL300000280304 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280304' /scratch/stefan/7769901/working/building/REAL300000280304 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280304 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280304/0 /scratch/stefan/7769901/working/building/REAL300000280304 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/432 `/scratch/stefan/7769901/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1) `REAL300000280304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280304 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 29, 29, 8, 1, 1, 1, 1, 33, 33, 33, 33, 33] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280304 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 97, 33, 97, 33, 33, 33, 33, 33, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 97, 33, 33, 33, 33, 1, 2, 2, 2, 1] 201 rigid atoms, others: [37, 41, 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, 38, 39, 40]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280304 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280304 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280304/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280304 Building REAL300000280305 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280305' /scratch/stefan/7769901/working/building/REAL300000280305 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280305 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280305/0 /scratch/stefan/7769901/working/building/REAL300000280305 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/433 `/scratch/stefan/7769901/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C) `REAL300000280305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280305 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [63, 46, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 37, 37, 37, 53, 53, 37, 37, 37, 37, 37, 73, 73, 73, 73, 73, 46, 46, 8, 1, 1, 1, 1, 37, 74, 37, 37, 37, 37] 402 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280305 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 73, 73, 37, 73, 37, 37, 37, 37, 37, 19, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 182, 182, 73, 37, 37, 37, 37, 1, 2, 1, 2, 2, 2] 402 rigid atoms, others: [39, 41, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 43, 44]) total number of confs: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280305 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280305 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280305/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280305 Building REAL300000280306 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280306' /scratch/stefan/7769901/working/building/REAL300000280306 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280306 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280306/0 /scratch/stefan/7769901/working/building/REAL300000280306 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/434 `/scratch/stefan/7769901/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1) `REAL300000280306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280306 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 55, 55, 55, 55, 55, 59, 59, 55, 56, 56, 56, 56, 56, 36, 36, 8, 1, 1, 1, 1, 55, 55, 55, 55] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280306 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 197, 101, 101, 55, 101, 55, 55, 55, 55, 55, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 197, 197, 101, 55, 55, 55, 55, 1, 2, 2, 2] 201 rigid atoms, others: [37, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280306 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280306 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280306/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280306 Building REAL300000280307 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280307' /scratch/stefan/7769901/working/building/REAL300000280307 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280307 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280307/0 /scratch/stefan/7769901/working/building/REAL300000280307 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/435 `/scratch/stefan/7769901/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C) `REAL300000280307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280307 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 35, 35, 35, 52, 52, 35, 35, 35, 35, 35, 74, 74, 74, 74, 74, 47, 47, 8, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280307 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 76, 76, 35, 76, 35, 35, 35, 35, 35, 19, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 76, 35, 35, 35, 35, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 46]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280307 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280307 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280307/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280307 Building REAL300000280308 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280308' /scratch/stefan/7769901/working/building/REAL300000280308 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280308 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280308/0 /scratch/stefan/7769901/working/building/REAL300000280308 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/436 `/scratch/stefan/7769901/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1) `REAL300000280308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280308 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 47, 47, 47, 47, 47, 35, 35, 9, 1, 1, 1, 1, 29, 29] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 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: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280308 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 94, 94, 29, 94, 29, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 94, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [36, 37, 13, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280308 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280308 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280308/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280308 Building REAL300000280309 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280309' /scratch/stefan/7769901/working/building/REAL300000280309 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280309 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280309/0 /scratch/stefan/7769901/working/building/REAL300000280309 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/437 `/scratch/stefan/7769901/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1) `REAL300000280309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280309 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 35, 19, 19, 35, 35, 19, 51, 51, 51, 51, 51, 28, 28, 8, 1, 1, 1, 1, 19, 19, 35, 35, 35, 19] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280309 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 103, 37, 37, 19, 37, 19, 19, 19, 19, 19, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 147, 147, 147, 147, 147, 103, 103, 37, 19, 19, 19, 19, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [39, 40, 44, 13, 16, 17, 18, 19, 20, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280309 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280309 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280309/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280309 Building REAL300000280310 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280310' /scratch/stefan/7769901/working/building/REAL300000280310 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280310 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280310/0 /scratch/stefan/7769901/working/building/REAL300000280310 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/438 `/scratch/stefan/7769901/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1CC) `REAL300000280310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280310 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 57, 69, 69, 69, 69, 69, 43, 43, 8, 1, 1, 1, 1, 33, 33, 33, 57, 57, 57, 57, 57] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280310 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 70, 70, 33, 70, 33, 33, 33, 33, 33, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 174, 174, 70, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [39, 40, 41, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 854 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280310 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280310 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280310/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280310 Building REAL300000280311 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280311' /scratch/stefan/7769901/working/building/REAL300000280311 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280311 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280311/0 /scratch/stefan/7769901/working/building/REAL300000280311 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/439 `/scratch/stefan/7769901/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1) `REAL300000280311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280311 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 32, 32, 8, 1, 1, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280311 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 106, 48, 108, 48, 48, 39, 48, 48, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 108, 48, 48, 48, 48, 2, 2, 2, 1] 201 rigid atoms, others: [40, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280311 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280311 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280311/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280311 Building REAL300000280312 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280312' /scratch/stefan/7769901/working/building/REAL300000280312 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280312 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280312/0 /scratch/stefan/7769901/working/building/REAL300000280312 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/440 `/scratch/stefan/7769901/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O) `REAL300000280312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280312 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.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: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 59, 59, 59, 59, 59, 33, 33, 8, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100] 402 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280312 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.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: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 103, 50, 103, 50, 50, 50, 50, 50, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 201, 201, 103, 50, 50, 50, 50, 1, 2, 2, 2, 1, 2] 402 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280312 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280312 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280312/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280312 Building REAL300000280313 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280313' /scratch/stefan/7769901/working/building/REAL300000280313 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280313 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280313/0 /scratch/stefan/7769901/working/building/REAL300000280313 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/441 `/scratch/stefan/7769901/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C) `REAL300000280313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280313 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 60, 60, 60, 60, 60, 40, 40, 10, 1, 1, 1, 1, 42, 42, 42, 42, 42] 190 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280313 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [190, 190, 88, 88, 42, 88, 42, 42, 42, 42, 42, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 190, 190, 88, 42, 42, 42, 42, 1, 1, 2, 2, 2] 190 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280313 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280313 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280313/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280313 Building REAL300000280314 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280314' /scratch/stefan/7769901/working/building/REAL300000280314 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280314 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280314/0 /scratch/stefan/7769901/working/building/REAL300000280314 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/442 `/scratch/stefan/7769901/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1) `REAL300000280314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280314 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 45, 45, 45, 45, 45, 45, 45, 45, 61, 61, 61, 61, 61, 35, 35, 8, 1, 1, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280314 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 97, 45, 97, 45, 45, 45, 45, 45, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 97, 45, 45, 45, 45, 2, 2, 2, 1] 201 rigid atoms, others: [40, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280314 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280314 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280314/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280314 Building REAL300000280315 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280315' /scratch/stefan/7769901/working/building/REAL300000280315 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280315 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280315/0 /scratch/stefan/7769901/working/building/REAL300000280315 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/443 `/scratch/stefan/7769901/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000280315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280315 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [43, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 25, 25, 17, 19, 25, 25, 25, 25, 25, 47, 47, 47, 47, 47, 38, 38, 10, 1, 1, 1, 1, 25, 25, 25] 140 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280315 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 72, 72, 25, 72, 25, 25, 25, 25, 25, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 72, 25, 25, 25, 25, 1, 1, 1] 140 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280315 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280315 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280315/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280315 Building REAL300000280316 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280316' /scratch/stefan/7769901/working/building/REAL300000280316 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280316 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280316/0 /scratch/stefan/7769901/working/building/REAL300000280316 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/444 `/scratch/stefan/7769901/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000280316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280316 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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: [42, 37, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 25, 25, 25, 25, 45, 45, 25, 25, 25, 52, 52, 52, 52, 52, 37, 37, 8, 1, 1, 1, 1, 25, 25, 25] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280316 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 68, 68, 25, 68, 25, 25, 25, 25, 25, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 68, 25, 25, 25, 25, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280316 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280316 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280316/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280316 Building REAL300000280317 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280317' /scratch/stefan/7769901/working/building/REAL300000280317 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280317 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280317/0 /scratch/stefan/7769901/working/building/REAL300000280317 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/445 `/scratch/stefan/7769901/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1) `REAL300000280317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280317 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 55, 55, 55, 55, 55, 55, 55, 54, 54, 54, 54, 54, 36, 36, 8, 1, 1, 1, 1, 55, 55] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 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: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280317 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 108, 55, 108, 55, 55, 55, 55, 55, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 108, 55, 55, 55, 55, 1, 1] 201 rigid atoms, others: [36, 37, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280317 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280317 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280317/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280317 Building REAL300000280318 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280318' /scratch/stefan/7769901/working/building/REAL300000280318 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280318 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280318/0 /scratch/stefan/7769901/working/building/REAL300000280318 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/446 `/scratch/stefan/7769901/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000280318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280318 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 34, 34, 8, 1, 1, 1, 1, 29, 29, 29] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280318 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 92, 92, 29, 92, 29, 29, 29, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 92, 29, 29, 29, 29, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280318 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280318 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280318/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280318 Building REAL300000280319 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280319' /scratch/stefan/7769901/working/building/REAL300000280319 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280319 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280319/0 /scratch/stefan/7769901/working/building/REAL300000280319 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/447 `/scratch/stefan/7769901/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F) `REAL300000280319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280319 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 61, 61, 61, 61, 61, 39, 39, 8, 1, 1, 1, 1, 55, 55, 55, 55, 55] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280319 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 104, 104, 55, 104, 55, 55, 55, 55, 55, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 104, 55, 55, 55, 55, 1, 1, 2, 2, 2] 201 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280319 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280319 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280319/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280319 Building REAL300000280320 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280320' /scratch/stefan/7769901/working/building/REAL300000280320 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280320 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280320/0 /scratch/stefan/7769901/working/building/REAL300000280320 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/448 `/scratch/stefan/7769901/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000280320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280320 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 54, 54, 31, 54, 54, 54, 54, 54, 54, 50, 50, 50, 50, 50, 34, 34, 8, 1, 1, 1, 1, 54, 54, 54] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280320 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 105, 105, 54, 105, 54, 54, 54, 54, 54, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 54, 54, 54, 54, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280320 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280320 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280320/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280320 Building REAL300000280321 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280321' /scratch/stefan/7769901/working/building/REAL300000280321 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280321 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280321/0 /scratch/stefan/7769901/working/building/REAL300000280321 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/449 `/scratch/stefan/7769901/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000280321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280321 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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: [42, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 37, 37, 29, 29, 29, 48, 48, 48, 48, 48, 40, 40, 10, 1, 1, 1, 1, 29, 29, 29] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280321 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 92, 92, 29, 92, 29, 29, 27, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 92, 29, 29, 29, 29, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280321 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280321 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280321/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280321 Building REAL300000280322 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280322' /scratch/stefan/7769901/working/building/REAL300000280322 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280322 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280322/0 /scratch/stefan/7769901/working/building/REAL300000280322 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/450 `/scratch/stefan/7769901/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1) `REAL300000280322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280322 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 51, 51, 27, 58, 58, 58, 58, 58, 38, 38, 8, 1, 1, 1, 1, 27, 27] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280322 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 61, 61, 27, 61, 27, 27, 27, 27, 27, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 145, 145, 61, 27, 27, 27, 27, 1, 1] 201 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280322 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280322 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280322/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280322 Building REAL300000280323 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280323' /scratch/stefan/7769901/working/building/REAL300000280323 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280323 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280323/0 /scratch/stefan/7769901/working/building/REAL300000280323 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/451 `/scratch/stefan/7769901/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000280323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280323 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [48, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 51, 51, 51, 51, 51, 51, 51, 51, 51, 59, 59, 59, 59, 59, 36, 36, 8, 1, 1, 1, 1, 51, 51, 51, 102] 402 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280323 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 105, 105, 51, 105, 51, 51, 51, 51, 51, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 51, 51, 51, 51, 1, 1, 1, 2] 402 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280323 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280323 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280323/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280323 Building REAL300000280324 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280324' /scratch/stefan/7769901/working/building/REAL300000280324 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280324 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280324/0 /scratch/stefan/7769901/working/building/REAL300000280324 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/452 `/scratch/stefan/7769901/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280324 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 41, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 29, 41, 41, 15, 15, 57, 57, 57, 57, 57, 41, 41, 10, 1, 1, 1, 1, 15, 15, 29, 29, 15, 15] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280324 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 54, 54, 15, 54, 15, 15, 15, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 133, 133, 133, 133, 133, 131, 131, 54, 15, 15, 15, 15, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 13, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280324 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280324 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280324/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280324 Building REAL300000280325 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280325' /scratch/stefan/7769901/working/building/REAL300000280325 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280325 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280325/0 /scratch/stefan/7769901/working/building/REAL300000280325 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/453 `/scratch/stefan/7769901/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300000280325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280325 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 37, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 54, 54, 54, 54, 54, 37, 37, 10, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 173 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280325 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 94, 94, 41, 94, 41, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 173, 173, 173, 173, 173, 173, 173, 94, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 173 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280325 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280325 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280325/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280325 Building REAL300000280326 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280326' /scratch/stefan/7769901/working/building/REAL300000280326 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280326 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280326/0 /scratch/stefan/7769901/working/building/REAL300000280326 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/454 `/scratch/stefan/7769901/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1) `REAL300000280326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280326 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 52, 52, 27, 58, 58, 58, 58, 58, 38, 38, 8, 1, 1, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280326 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 142, 59, 59, 27, 59, 27, 27, 27, 27, 27, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 142, 142, 59, 27, 27, 27, 27, 1, 2, 2, 2, 1] 201 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 907 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280326 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280326 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280326/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280326 Building REAL300000280327 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280327' /scratch/stefan/7769901/working/building/REAL300000280327 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280327 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280327/0 /scratch/stefan/7769901/working/building/REAL300000280327 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/455 `/scratch/stefan/7769901/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000280327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280327 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 39, 39, 27, 27, 39, 39, 39, 39, 39, 57, 57, 57, 57, 57, 39, 39, 10, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39] 173 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280327 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 87, 87, 39, 87, 39, 39, 38, 39, 39, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 173, 173, 173, 173, 173, 173, 173, 87, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2] 173 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280327 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280327 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280327/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280327 Building REAL300000280328 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280328' /scratch/stefan/7769901/working/building/REAL300000280328 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280328 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280328/0 /scratch/stefan/7769901/working/building/REAL300000280328 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/456 `/scratch/stefan/7769901/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1) `REAL300000280328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280328 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 51, 51, 51, 51, 51, 36, 36, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 337 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280328 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 101, 29, 101, 29, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 101, 29, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [39, 13, 46, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 728 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280328 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280328 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280328/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280328 Building REAL300000280329 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280329' /scratch/stefan/7769901/working/building/REAL300000280329 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280329 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280329/0 /scratch/stefan/7769901/working/building/REAL300000280329 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/457 `/scratch/stefan/7769901/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F) `REAL300000280329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280329 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 57, 57, 57, 57, 57, 35, 35, 8, 1, 1, 1, 1, 55, 55] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280329 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 98, 98, 55, 98, 55, 55, 55, 55, 55, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 98, 55, 55, 55, 55, 1, 1] 201 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280329 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280329 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280329/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280329 Building REAL300000280330 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280330' /scratch/stefan/7769901/working/building/REAL300000280330 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280330 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280330/0 /scratch/stefan/7769901/working/building/REAL300000280330 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/458 `/scratch/stefan/7769901/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C) `REAL300000280330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280330 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 49, 49, 49, 49, 49, 33, 33, 10, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41] 171 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280330 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [171, 171, 91, 91, 41, 91, 41, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 171, 171, 171, 171, 171, 171, 171, 91, 41, 41, 41, 41, 1, 1, 2, 2, 2, 2, 2, 2] 171 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280330 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280330 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280330/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280330 Building REAL300000280331 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280331' /scratch/stefan/7769901/working/building/REAL300000280331 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280331 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280331/0 /scratch/stefan/7769901/working/building/REAL300000280331 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/459 `/scratch/stefan/7769901/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F) `REAL300000280331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280331 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 47, 47, 47, 73, 73, 47, 47, 47, 47, 47, 52, 52, 52, 52, 52, 31, 31, 8, 1, 1, 1, 1, 47, 47, 47, 47, 47] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280331 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 85, 85, 47, 85, 47, 47, 47, 47, 47, 25, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 85, 47, 47, 47, 47, 1, 2, 2, 2, 1] 201 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280331 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280331 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280331/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280331 Building REAL300000280332 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280332' /scratch/stefan/7769901/working/building/REAL300000280332 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280332 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280332/0 /scratch/stefan/7769901/working/building/REAL300000280332 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/460 `/scratch/stefan/7769901/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F) `REAL300000280332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280332 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 40, 40, 40, 40, 40, 40, 70, 70, 40, 40, 50, 50, 50, 50, 50, 34, 34, 6, 1, 1, 1, 1, 40, 40, 40, 40, 40] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280332 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 69, 69, 40, 69, 40, 40, 40, 40, 40, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 164, 164, 69, 40, 40, 40, 40, 1, 2, 2, 2, 1] 201 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280332 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280332 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280332/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280332 Building REAL300000280333 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280333' /scratch/stefan/7769901/working/building/REAL300000280333 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280333 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280333/0 /scratch/stefan/7769901/working/building/REAL300000280333 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/461 `/scratch/stefan/7769901/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC)C(C(=O)[O-])=C1) `REAL300000280333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280333 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 18, 18, 18, 18, 39, 18, 18, 22, 22, 18, 37, 37, 37, 37, 37, 26, 26, 6, 1, 1, 1, 1, 18, 18, 39, 39, 39, 39, 39, 18] 162 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280333 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(CC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 81, 36, 36, 18, 36, 18, 18, 18, 18, 18, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 1, 1, 3, 3, 1, 85, 85, 85, 85, 85, 81, 81, 36, 18, 18, 18, 18, 1, 1, 4, 4, 4, 4, 4, 1] 162 rigid atoms, others: [39, 40, 13, 46, 16, 17, 18, 19, 20, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280333 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280333 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280333/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280333 Building REAL300000280334 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280334' /scratch/stefan/7769901/working/building/REAL300000280334 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280334 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280334/0 /scratch/stefan/7769901/working/building/REAL300000280334 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/462 `/scratch/stefan/7769901/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(CC)C(C(=O)[O-])=C1) `REAL300000280334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280334 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(CC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 57, 25, 25, 25, 25, 25, 41, 41, 41, 41, 41, 25, 25, 6, 1, 1, 1, 1, 25, 57, 57, 57, 57, 57, 25] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280334 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CN(CC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 47, 47, 25, 47, 25, 25, 22, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 4, 1, 1, 2, 2, 1, 120, 120, 120, 120, 120, 112, 112, 47, 25, 25, 25, 25, 1, 4, 4, 4, 4, 4, 1] 201 rigid atoms, others: [38, 44, 13, 16, 17, 18, 19, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280334 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280334 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280334/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280334 Building REAL300000280335 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280335' /scratch/stefan/7769901/working/building/REAL300000280335 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280335 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280335/0 /scratch/stefan/7769901/working/building/REAL300000280335 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/463 `/scratch/stefan/7769901/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1) `REAL300000280335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280335 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 25, 25, 25, 25, 48, 48, 25, 25, 25, 51, 51, 51, 51, 51, 37, 37, 8, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280335 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 68, 68, 25, 68, 25, 25, 25, 25, 25, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 68, 25, 25, 25, 25, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [38, 39, 43, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280335 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280335 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280335/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280335 Building REAL300000280336 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280336' /scratch/stefan/7769901/working/building/REAL300000280336 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280336 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280336/0 /scratch/stefan/7769901/working/building/REAL300000280336 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/464 `/scratch/stefan/7769901/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C) `REAL300000280336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280336 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 30, 30, 30, 53, 53, 30, 30, 30, 30, 30, 69, 69, 69, 69, 69, 44, 44, 8, 1, 1, 1, 1, 30, 30, 30, 30, 30] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280336 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 65, 65, 30, 65, 30, 30, 30, 30, 30, 16, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 65, 30, 30, 30, 30, 1, 1, 2, 2, 2] 201 rigid atoms, others: [39, 40, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 877 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280336 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280336 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280336/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280336 Building REAL300000280337 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280337' /scratch/stefan/7769901/working/building/REAL300000280337 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280337 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280337/0 /scratch/stefan/7769901/working/building/REAL300000280337 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/465 `/scratch/stefan/7769901/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000280337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280337 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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: [52, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 41, 41, 41, 41, 41, 71, 71, 41, 41, 60, 60, 60, 60, 60, 34, 34, 8, 1, 1, 1, 1, 41, 41, 41] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280337 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 72, 72, 41, 72, 41, 41, 41, 41, 41, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 157, 157, 72, 41, 41, 41, 41, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 834 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280337 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280337 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280337/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280337 Building REAL300000280338 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280338' /scratch/stefan/7769901/working/building/REAL300000280338 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280338 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280338/0 /scratch/stefan/7769901/working/building/REAL300000280338 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/466 `/scratch/stefan/7769901/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1) `REAL300000280338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280338 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 51, 51, 51, 51, 51, 38, 38, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280338 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 101, 29, 101, 29, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 101, 29, 29, 29, 29, 1, 2, 2, 2, 1] 201 rigid atoms, others: [39, 43, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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 /scratch/stefan/7769901/working/building/REAL300000280338 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280338 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280338/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280338 Building REAL300000280339 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280339' /scratch/stefan/7769901/working/building/REAL300000280339 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280339 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280339/0 /scratch/stefan/7769901/working/building/REAL300000280339 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/467 `/scratch/stefan/7769901/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300000280339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280339 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 60, 60, 60, 60, 60, 60, 60, 60, 41, 41, 41, 41, 41, 31, 31, 8, 1, 1, 1, 1, 60, 60, 60] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280339 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 114, 114, 60, 114, 60, 60, 60, 60, 60, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 60, 60, 60, 60, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280339 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280339 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280339/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280339 Building REAL300000280340 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280340' /scratch/stefan/7769901/working/building/REAL300000280340 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280340 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280340/0 /scratch/stefan/7769901/working/building/REAL300000280340 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/468 `/scratch/stefan/7769901/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC) `REAL300000280340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280340 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens 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, 35, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 45, 45, 29, 45, 45, 45, 45, 45, 45, 69, 59, 59, 59, 59, 59, 35, 35, 8, 1, 1, 1, 1, 45, 45, 45, 69, 69, 69] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280340 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 94, 94, 45, 94, 45, 45, 45, 45, 45, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 201, 201, 201, 201, 201, 192, 192, 94, 45, 45, 45, 45, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [39, 40, 41, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280340 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280340 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280340/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280340 Building REAL300000280341 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280341' /scratch/stefan/7769901/working/building/REAL300000280341 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280341 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280341/0 /scratch/stefan/7769901/working/building/REAL300000280341 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/469 `/scratch/stefan/7769901/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000280341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280341 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 36, 36, 8, 1, 1, 1, 1, 47] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280341 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 105, 105, 47, 105, 47, 47, 47, 47, 47, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 105, 47, 47, 47, 47, 1] 201 rigid atoms, others: [37, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280341 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280341 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280341/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280341 Building REAL300000280342 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280342' /scratch/stefan/7769901/working/building/REAL300000280342 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280342 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280342/0 /scratch/stefan/7769901/working/building/REAL300000280342 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/470 `/scratch/stefan/7769901/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(CC)OC(C(=O)[O-])=C1) `REAL300000280342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280342 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(CC)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [47, 37, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 43, 43, 74, 43, 43, 43, 43, 43, 43, 57, 57, 57, 57, 57, 37, 37, 8, 1, 1, 1, 1, 74, 74, 74, 74, 74, 43] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 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: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280342 none CCCNC(=O)C1=CC=CC=C1[N-]S(=O)(=O)C1=C(CC)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [195, 176, 84, 84, 43, 84, 43, 43, 42, 43, 43, 21, 7, 1, 7, 7, 1, 1, 1, 5, 1, 1, 1, 2, 2, 1, 199, 199, 199, 199, 199, 176, 176, 84, 43, 43, 43, 43, 5, 5, 6, 6, 6, 1] 201 rigid atoms, others: [43, 13, 16, 17, 18, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 834 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280342 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280342 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280342/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280342 Building REAL300000280343 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280343' /scratch/stefan/7769901/working/building/REAL300000280343 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280343 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280343/0 /scratch/stefan/7769901/working/building/REAL300000280343 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/471 `/scratch/stefan/7769901/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1F) `REAL300000280343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280343 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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, 1, 2, 2, 2, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280343 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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, 29, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280343 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280343 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280343/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280343 Building REAL300000280344 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280344' /scratch/stefan/7769901/working/building/REAL300000280344 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280344 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280344/0 /scratch/stefan/7769901/working/building/REAL300000280344 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/472 `/scratch/stefan/7769901/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280344 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 37, 36] set([32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280344 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 11 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280344 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280344 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280344/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280344 Building REAL300000280345 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280345' /scratch/stefan/7769901/working/building/REAL300000280345 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280345 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280345/0 /scratch/stefan/7769901/working/building/REAL300000280345 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/473 `/scratch/stefan/7769901/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280345 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 37] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280345 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280345 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280345/1 /scratch/stefan/7769901/working/building/REAL300000280345 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/474 `/scratch/stefan/7769901/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280345.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280345 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280345 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280345 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280345 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280345/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280345/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280345 Building REAL300000280346 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280346' /scratch/stefan/7769901/working/building/REAL300000280346 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280346 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280346/0 /scratch/stefan/7769901/working/building/REAL300000280346 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/475 `/scratch/stefan/7769901/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280346 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 23, 57, 57, 57, 47, 57, 57, 57, 57, 57, 57, 3, 3, 3, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 29, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280346 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 57, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280346 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280346/1 /scratch/stefan/7769901/working/building/REAL300000280346 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/476 `/scratch/stefan/7769901/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280346.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280346 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 59, 59, 59, 49, 59, 59, 59, 59, 59, 59, 4, 4, 4, 1, 1, 1, 23, 59, 59, 59, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280346 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 59, 26, 9, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280346 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280346 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280346/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280346/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280346 Building REAL300000280347 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280347' /scratch/stefan/7769901/working/building/REAL300000280347 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280347 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280347/0 /scratch/stefan/7769901/working/building/REAL300000280347 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/477 `/scratch/stefan/7769901/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280347 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 46, 46, 46, 17, 46, 46, 46, 46, 46, 46, 1, 1, 3, 3, 1, 1, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 46 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 41, 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]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280347 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 46 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 126 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280347 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280347/1 /scratch/stefan/7769901/working/building/REAL300000280347 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/478 `/scratch/stefan/7769901/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280347.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280347 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 46, 46, 46, 44, 46, 46, 46, 46, 46, 46, 1, 1, 3, 3, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 46 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 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]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280347 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 46 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 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, 40, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 117 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280347 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280347 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280347/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280347/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280347 Building REAL300000280348 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280348' /scratch/stefan/7769901/working/building/REAL300000280348 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280348 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280348/0 /scratch/stefan/7769901/working/building/REAL300000280348 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/479 `/scratch/stefan/7769901/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280348 none CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280348 none CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 40, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280348 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280348 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280348/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280348 Building REAL300000280349 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280349' /scratch/stefan/7769901/working/building/REAL300000280349 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280349 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280349/0 /scratch/stefan/7769901/working/building/REAL300000280349 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/480 `/scratch/stefan/7769901/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280349 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280349 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 9, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280349 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280349/1 /scratch/stefan/7769901/working/building/REAL300000280349 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/481 `/scratch/stefan/7769901/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280349.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280349 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280349 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280349 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280349 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280349/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280349/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280349 Building REAL300000280350 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280350' /scratch/stefan/7769901/working/building/REAL300000280350 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280350 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280350/0 /scratch/stefan/7769901/working/building/REAL300000280350 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/482 `/scratch/stefan/7769901/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1Cl) `REAL300000280350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280350 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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 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, 2, 2, 2, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280350 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280350 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280350/1 /scratch/stefan/7769901/working/building/REAL300000280350 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/483 `/scratch/stefan/7769901/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1Cl) `REAL300000280350.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280350 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 19, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280350 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [32, 33, 34, 9, 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, 35, 21, 22, 23, 24, 25, 36]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280350 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280350 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280350/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280350/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280350 Building REAL300000280351 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280351' /scratch/stefan/7769901/working/building/REAL300000280351 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280351 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280351/0 /scratch/stefan/7769901/working/building/REAL300000280351 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/484 `/scratch/stefan/7769901/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1C) `REAL300000280351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280351 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2] 14 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 24, 25, 29, 30] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280351 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 14 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280351 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280351/1 /scratch/stefan/7769901/working/building/REAL300000280351 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/485 `/scratch/stefan/7769901/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1C) `REAL300000280351.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280351 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280351 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280351 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280351 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280351/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280351/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280351 Building REAL300000280352 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280352' /scratch/stefan/7769901/working/building/REAL300000280352 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280352 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280352/0 /scratch/stefan/7769901/working/building/REAL300000280352 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/486 `/scratch/stefan/7769901/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280352 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280352 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 10, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52] 52 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280352 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280352 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280352/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280352 Building REAL300000280353 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280353' /scratch/stefan/7769901/working/building/REAL300000280353 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280353 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280353/0 /scratch/stefan/7769901/working/building/REAL300000280353 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/487 `/scratch/stefan/7769901/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280353 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 13, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 8, 8, 4, 4, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 80 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 43, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280353 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 53, 39, 39, 39, 39, 22, 9, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 80, 80, 53, 53, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 80 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280353 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280353/1 /scratch/stefan/7769901/working/building/REAL300000280353 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/488 `/scratch/stefan/7769901/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280353.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280353 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [11, 4, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 4, 4, 4, 4, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 72 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 41, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280353 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 69, 72, 46, 46, 46, 46, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 72, 72, 72, 72, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280353 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280353 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280353/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280353/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280353 Building REAL300000280354 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280354' /scratch/stefan/7769901/working/building/REAL300000280354 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280354 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280354/0 /scratch/stefan/7769901/working/building/REAL300000280354 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/489 `/scratch/stefan/7769901/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280354 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280354 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [46, 46, 46, 46, 46, 46, 28, 11, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46] 46 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 33]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280354 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280354 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280354/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280354 Building REAL300000280355 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280355' /scratch/stefan/7769901/working/building/REAL300000280355 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280355 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280355/0 /scratch/stefan/7769901/working/building/REAL300000280355 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/490 `/scratch/stefan/7769901/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280355 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280355 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 9, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 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, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280355 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280355/1 /scratch/stefan/7769901/working/building/REAL300000280355 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/491 `/scratch/stefan/7769901/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280355.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280355 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 7, 7, 7, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280355 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 20, 9, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280355 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280355 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280355/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280355/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280355 Building REAL300000280356 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280356' /scratch/stefan/7769901/working/building/REAL300000280356 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280356 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280356/0 /scratch/stefan/7769901/working/building/REAL300000280356 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/492 `/scratch/stefan/7769901/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280356 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 13, 23, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 32, 32, 17, 32, 32, 32, 32, 32, 32, 1, 1, 13, 13, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 122 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 41, 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]) total number of confs: 143 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280356 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 63, 32, 18, 32, 32, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 122, 122, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 122 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 510 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280356 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280356 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280356/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280356 Building REAL300000280357 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280357' /scratch/stefan/7769901/working/building/REAL300000280357 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280357 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280357/0 /scratch/stefan/7769901/working/building/REAL300000280357 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/493 `/scratch/stefan/7769901/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280357 none CN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 38, 19, 20, 21, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280357 none CN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 38, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280357 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280357/1 /scratch/stefan/7769901/working/building/REAL300000280357 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/494 `/scratch/stefan/7769901/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280357.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280357 none CN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 37, 19, 20, 21, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280357 none CN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280357 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280357 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280357/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280357/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280357 Building REAL300000280358 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280358' /scratch/stefan/7769901/working/building/REAL300000280358 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280358 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280358/0 /scratch/stefan/7769901/working/building/REAL300000280358 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/495 `/scratch/stefan/7769901/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280358 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 2, 1, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 29, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280358 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 46, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280358 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280358 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280358/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280358 Building REAL300000280359 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280359' /scratch/stefan/7769901/working/building/REAL300000280359 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280359 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280359/0 /scratch/stefan/7769901/working/building/REAL300000280359 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/496 `/scratch/stefan/7769901/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280359 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 25, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 2, 2, 2, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280359 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 29, 10, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280359 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280359 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280359/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280359 Building REAL300000280360 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280360' /scratch/stefan/7769901/working/building/REAL300000280360 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280360 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280360/0 /scratch/stefan/7769901/working/building/REAL300000280360 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/497 `/scratch/stefan/7769901/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280360 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 5, 23, 23, 23, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 2, 2, 2, 1, 2, 2, 2, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280360 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23] 23 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280360 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280360 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280360/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280360 Building REAL300000280361 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280361' /scratch/stefan/7769901/working/building/REAL300000280361 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280361 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280361/0 /scratch/stefan/7769901/working/building/REAL300000280361 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/498 `/scratch/stefan/7769901/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CS1) `REAL300000280361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280361 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 33, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280361 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 33]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280361 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280361/1 /scratch/stefan/7769901/working/building/REAL300000280361 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/499 `/scratch/stefan/7769901/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CS1) `REAL300000280361.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280361 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 18 rigid atoms, others: [1, 34, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280361 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 18 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 24]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280361 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280361 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280361/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280361/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280361 Building REAL300000280362 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280362' /scratch/stefan/7769901/working/building/REAL300000280362 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280362 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280362/0 /scratch/stefan/7769901/working/building/REAL300000280362 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/500 `/scratch/stefan/7769901/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280362 none COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 51 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 21, 22, 23, 29, 30] set([0, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280362 none COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 29, 29, 29, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 51, 51, 51, 51, 51, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 51 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280362 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280362 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280362/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280362 Building REAL300000280363 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280363' /scratch/stefan/7769901/working/building/REAL300000280363 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280363 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280363/0 /scratch/stefan/7769901/working/building/REAL300000280363 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/501 `/scratch/stefan/7769901/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280363 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36] set([0, 2, 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: 40 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280363 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280363 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280363/1 /scratch/stefan/7769901/working/building/REAL300000280363 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/502 `/scratch/stefan/7769901/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280363.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280363 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 3, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 10, 11, 12, 35, 36] set([0, 2, 8, 9, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280363 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280363 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280363 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280363/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280363/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280363 Building REAL300000280364 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280364' /scratch/stefan/7769901/working/building/REAL300000280364 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280364 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280364/0 /scratch/stefan/7769901/working/building/REAL300000280364 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/503 `/scratch/stefan/7769901/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280364 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 1, 1, 1, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 31] set([0, 7, 8, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280364 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 9, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280364 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280364/1 /scratch/stefan/7769901/working/building/REAL300000280364 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/504 `/scratch/stefan/7769901/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280364.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280364 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 18, 45, 45, 45, 27, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280364 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 28, 10, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280364 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280364 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280364/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280364/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280364 Building REAL300000280365 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280365' /scratch/stefan/7769901/working/building/REAL300000280365 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280365 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280365/0 /scratch/stefan/7769901/working/building/REAL300000280365 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/505 `/scratch/stefan/7769901/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280365 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 23, 54, 54, 54, 53, 54, 54, 54, 54, 54, 54, 4, 4, 4, 1, 1, 2, 2, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54] 84 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280365 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 54, 54, 54, 31, 54, 54, 80, 84, 84, 54, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 54, 54, 80, 80, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280365 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280365/1 /scratch/stefan/7769901/working/building/REAL300000280365 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/506 `/scratch/stefan/7769901/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280365.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280365 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 7, 7, 7, 15, 25, 25, 25, 19, 25, 25, 25, 25, 25, 25, 4, 4, 4, 1, 1, 2, 2, 1, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280365 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 25, 25, 25, 19, 25, 25, 30, 30, 30, 25, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 25, 25, 30, 30, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280365 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280365 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280365/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280365/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280365 Building REAL300000280366 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280366' /scratch/stefan/7769901/working/building/REAL300000280366 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280366 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280366/0 /scratch/stefan/7769901/working/building/REAL300000280366 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/507 `/scratch/stefan/7769901/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1) `REAL300000280366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280366 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 38, 21, 22, 23, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280366 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280366 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280366/1 /scratch/stefan/7769901/working/building/REAL300000280366 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/508 `/scratch/stefan/7769901/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1) `REAL300000280366.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280366 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 8 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 38, 21, 22, 23, 26, 27, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280366 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 8 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280366 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280366 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280366/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280366/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280366 Building REAL300000280367 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280367' /scratch/stefan/7769901/working/building/REAL300000280367 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280367 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280367/0 /scratch/stefan/7769901/working/building/REAL300000280367 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/509 `/scratch/stefan/7769901/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280367 none O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)NC2=CC=C3OCCCOC3=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.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 5, 5, 5, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 44, 33, 32, 26, 27, 28, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280367 none O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)NC2=CC=C3OCCCOC3=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.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 24, 24, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24] 24 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280367 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280367/1 /scratch/stefan/7769901/working/building/REAL300000280367 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/510 `/scratch/stefan/7769901/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280367.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280367 none O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=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.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 43, 32, 26, 27, 28, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280367 none O=C([O-])C1=CC2=C(CCC2)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=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.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 47, 47, 29, 9, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280367 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280367 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280367/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280367/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280367 Building REAL300000280368 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280368' /scratch/stefan/7769901/working/building/REAL300000280368 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280368 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280368/0 /scratch/stefan/7769901/working/building/REAL300000280368 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/511 `/scratch/stefan/7769901/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1) `REAL300000280368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280368 none CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 36, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280368 none CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 24, 10, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280368 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280368/1 /scratch/stefan/7769901/working/building/REAL300000280368 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/512 `/scratch/stefan/7769901/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1) `REAL300000280368.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280368 none CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 32 rigid atoms, others: [0, 1, 2, 3, 37, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280368 none CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 23, 9, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 32 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280368 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280368 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280368/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280368/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280368 Building REAL300000280369 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280369' /scratch/stefan/7769901/working/building/REAL300000280369 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280369 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280369/0 /scratch/stefan/7769901/working/building/REAL300000280369 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/513 `/scratch/stefan/7769901/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280369 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 24, 81, 81, 81, 37, 81, 81, 81, 81, 81, 81, 1, 2, 2, 2, 1, 2, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1] 162 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 40, 25, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280369 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [81, 81, 81, 81, 81, 81, 81, 81, 81, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 162, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81] 162 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 25, 26, 27, 28, 29, 30]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280369 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280369/1 /scratch/stefan/7769901/working/building/REAL300000280369 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/514 `/scratch/stefan/7769901/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280369.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280369 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 3, 1, 1, 1, 1, 7, 7, 7, 18, 50, 50, 50, 46, 50, 50, 50, 50, 50, 50, 1, 2, 2, 2, 1, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 41, 25, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280369 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 11, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 100 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 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, 41, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280369 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280369 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280369/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280369/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280369 Building REAL300000280370 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280370' /scratch/stefan/7769901/working/building/REAL300000280370 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280370 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280370/0 /scratch/stefan/7769901/working/building/REAL300000280370 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/515 `/scratch/stefan/7769901/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1OCC(=O)[O-]) `REAL300000280370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280370 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 28, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 8, 34, 59, 59, 2, 2, 2, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 34, 34] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 19, 20, 21, 22, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280370 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens 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, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 15, 15, 100, 201, 201, 201, 29, 29, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280370 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280370 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280370/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280370 Building REAL300000280371 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280371' /scratch/stefan/7769901/working/building/REAL300000280371 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280371 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280371/0 /scratch/stefan/7769901/working/building/REAL300000280371 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/516 `/scratch/stefan/7769901/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280371 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 5, 5, 5, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280371 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 20, 9, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280371 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280371/1 /scratch/stefan/7769901/working/building/REAL300000280371 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/517 `/scratch/stefan/7769901/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280371.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280371 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280371 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 29, 20, 9, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280371 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280371 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280371/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280371/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280371 Building REAL300000280372 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280372' /scratch/stefan/7769901/working/building/REAL300000280372 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280372 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280372/0 /scratch/stefan/7769901/working/building/REAL300000280372 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/518 `/scratch/stefan/7769901/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F) `REAL300000280372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280372 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 78, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 48, 48, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 41, 24, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280372 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 201, 201, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 41, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280372 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280372/1 /scratch/stefan/7769901/working/building/REAL300000280372 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/519 `/scratch/stefan/7769901/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F) `REAL300000280372.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280372 none O=C([O-])COC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [53, 36, 53, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 36, 36, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 131 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 24, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280372 none O=C([O-])COC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 86, 21, 21, 21, 21, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 131, 131, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 131 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280372 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280372 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280372/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280372/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280372 Building REAL300000280373 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280373' /scratch/stefan/7769901/working/building/REAL300000280373 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280373 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280373/0 /scratch/stefan/7769901/working/building/REAL300000280373 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/520 `/scratch/stefan/7769901/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280373 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 66 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280373 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 49, 25, 25, 25, 25, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 35, 35, 66, 66, 66, 66, 66, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 66 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 256 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280373 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280373 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280373/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280373 Building REAL300000280374 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280374' /scratch/stefan/7769901/working/building/REAL300000280374 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280374 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280374/0 /scratch/stefan/7769901/working/building/REAL300000280374 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/521 `/scratch/stefan/7769901/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1) `REAL300000280374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280374 none CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 37, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280374 none CC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 17, 9, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280374 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280374/1 /scratch/stefan/7769901/working/building/REAL300000280374 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/522 `/scratch/stefan/7769901/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1) `REAL300000280374.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280374 none CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 36, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280374 none CC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 18, 9, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 22 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280374 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280374 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280374/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280374/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280374 Building REAL300000280375 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280375' /scratch/stefan/7769901/working/building/REAL300000280375 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280375 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280375/0 /scratch/stefan/7769901/working/building/REAL300000280375 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/523 `/scratch/stefan/7769901/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(Cl)=C1) `REAL300000280375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280375 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280375 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 20, 22, 22, 20, 10, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 22 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280375 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280375/1 /scratch/stefan/7769901/working/building/REAL300000280375 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/524 `/scratch/stefan/7769901/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(Cl)=C1) `REAL300000280375.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280375 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 37] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280375 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 17, 19, 19, 17, 9, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280375 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280375 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280375/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280375/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280375 Building REAL300000280376 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280376' /scratch/stefan/7769901/working/building/REAL300000280376 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280376 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280376/0 /scratch/stefan/7769901/working/building/REAL300000280376 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/525 `/scratch/stefan/7769901/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F) `REAL300000280376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280376 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280376 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 21, 9, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280376 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280376/1 /scratch/stefan/7769901/working/building/REAL300000280376 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/526 `/scratch/stefan/7769901/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F) `REAL300000280376.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280376 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280376 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 45, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45] 45 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280376 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280376 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280376/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280376/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280376 Building REAL300000280377 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280377' /scratch/stefan/7769901/working/building/REAL300000280377 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280377 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280377/0 /scratch/stefan/7769901/working/building/REAL300000280377 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/527 `/scratch/stefan/7769901/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)S1) `REAL300000280377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280377 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49] 49 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280377 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 30, 11, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280377 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280377 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280377/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280377 Building REAL300000280378 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280378' /scratch/stefan/7769901/working/building/REAL300000280378 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280378 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280378/0 /scratch/stefan/7769901/working/building/REAL300000280378 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/528 `/scratch/stefan/7769901/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280378 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 37] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280378 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280378 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280378/1 /scratch/stefan/7769901/working/building/REAL300000280378 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/529 `/scratch/stefan/7769901/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280378.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280378 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280378 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280378 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280378 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280378/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280378/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280378 Building REAL300000280379 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280379' /scratch/stefan/7769901/working/building/REAL300000280379 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280379 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280379/0 /scratch/stefan/7769901/working/building/REAL300000280379 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/530 `/scratch/stefan/7769901/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F) `REAL300000280379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280379 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 7, 7, 7, 25, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 2, 2, 2, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280379 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 27, 9, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1] 54 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280379 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280379 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280379/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280379 Building REAL300000280380 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280380' /scratch/stefan/7769901/working/building/REAL300000280380 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280380 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280380/0 /scratch/stefan/7769901/working/building/REAL300000280380 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/531 `/scratch/stefan/7769901/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(F)=C1) `REAL300000280380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280380 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280380 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 10, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40] 40 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280380 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280380/1 /scratch/stefan/7769901/working/building/REAL300000280380 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/532 `/scratch/stefan/7769901/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(F)=C1) `REAL300000280380.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280380 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 22, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 22, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 37] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280380 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280380 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280380 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280380/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280380/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280380 Building REAL300000280381 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280381' /scratch/stefan/7769901/working/building/REAL300000280381 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280381 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280381/0 /scratch/stefan/7769901/working/building/REAL300000280381 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/533 `/scratch/stefan/7769901/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1Cl) `REAL300000280381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280381 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280381 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280381 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280381/1 /scratch/stefan/7769901/working/building/REAL300000280381 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/534 `/scratch/stefan/7769901/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1Cl) `REAL300000280381.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280381 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280381 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28] 28 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280381 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280381 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280381/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280381/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280381 Building REAL300000280382 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280382' /scratch/stefan/7769901/working/building/REAL300000280382 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280382 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280382/0 /scratch/stefan/7769901/working/building/REAL300000280382 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/535 `/scratch/stefan/7769901/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280382 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 5, 5, 5, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280382 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 9, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280382 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280382/1 /scratch/stefan/7769901/working/building/REAL300000280382 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/536 `/scratch/stefan/7769901/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280382.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280382 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280382 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 9, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280382 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280382 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280382/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280382/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280382 Building REAL300000280383 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280383' /scratch/stefan/7769901/working/building/REAL300000280383 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280383 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280383/0 /scratch/stefan/7769901/working/building/REAL300000280383 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/537 `/scratch/stefan/7769901/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(F)=C1F) `REAL300000280383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280383 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 31, 31, 31, 16, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280383 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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 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, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 31 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280383 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280383/1 /scratch/stefan/7769901/working/building/REAL300000280383 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/538 `/scratch/stefan/7769901/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(F)=C1F) `REAL300000280383.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280383 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 39, 39, 39, 16, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 25, 21, 22, 23, 24, 36, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280383 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39] 39 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280383 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280383 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280383/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280383/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280383 Building REAL300000280384 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280384' /scratch/stefan/7769901/working/building/REAL300000280384 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280384 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280384/0 /scratch/stefan/7769901/working/building/REAL300000280384 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/539 `/scratch/stefan/7769901/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280384 none O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280384 none O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39, 26, 27, 28, 29]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280384 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280384/1 /scratch/stefan/7769901/working/building/REAL300000280384 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/540 `/scratch/stefan/7769901/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280384.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280384 none O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280384 none O=C([O-])C1=CC([N+](=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 38, 26, 27, 28]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280384 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280384 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280384/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280384/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280384 Building REAL300000280385 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280385' /scratch/stefan/7769901/working/building/REAL300000280385 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280385 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280385/0 /scratch/stefan/7769901/working/building/REAL300000280385 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/541 `/scratch/stefan/7769901/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280385 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1] 92 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280385 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [46, 46, 46, 46, 46, 46, 46, 46, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 92, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46] 92 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280385 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280385/1 /scratch/stefan/7769901/working/building/REAL300000280385 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/542 `/scratch/stefan/7769901/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1) `REAL300000280385.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280385 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 4, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280385 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 37]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280385 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280385 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280385/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280385/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280385 Building REAL300000280386 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280386' /scratch/stefan/7769901/working/building/REAL300000280386 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280386 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280386/0 /scratch/stefan/7769901/working/building/REAL300000280386 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/543 `/scratch/stefan/7769901/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280386 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280386 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280386 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280386/1 /scratch/stefan/7769901/working/building/REAL300000280386 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/544 `/scratch/stefan/7769901/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1) `REAL300000280386.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280386 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 39, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280386 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 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, 39, 38, 23, 24, 25, 26, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280386 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280386 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280386/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280386/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280386 Building REAL300000280387 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280387' /scratch/stefan/7769901/working/building/REAL300000280387 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280387 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280387/0 /scratch/stefan/7769901/working/building/REAL300000280387 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/545 `/scratch/stefan/7769901/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280387 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280387 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 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, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280387 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280387/1 /scratch/stefan/7769901/working/building/REAL300000280387 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/546 `/scratch/stefan/7769901/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280387.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280387 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [0, 1, 2, 3, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280387 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280387 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280387 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280387/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280387/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280387 Building REAL300000280388 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280388' /scratch/stefan/7769901/working/building/REAL300000280388 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280388 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280388/0 /scratch/stefan/7769901/working/building/REAL300000280388 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/547 `/scratch/stefan/7769901/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1F) `REAL300000280388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280388 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 29, 29, 29, 16, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 40, 19, 20, 21, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280388 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 40, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280388 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280388 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280388/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280388 Building REAL300000280389 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280389' /scratch/stefan/7769901/working/building/REAL300000280389 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280389 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280389/0 /scratch/stefan/7769901/working/building/REAL300000280389 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/548 `/scratch/stefan/7769901/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280389 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280389 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 26, 26, 26, 26, 26, 23, 10, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 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, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280389 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280389 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280389/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280389 Building REAL300000280390 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280390' /scratch/stefan/7769901/working/building/REAL300000280390 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280390 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280390/0 /scratch/stefan/7769901/working/building/REAL300000280390 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/549 `/scratch/stefan/7769901/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1C) `REAL300000280390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280390 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2] 16 rigid atoms, others: [0, 1, 2, 3, 4, 40, 19, 20, 21, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280390 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43]) total number of confs: 45 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280390 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280390 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280390/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280390 Building REAL300000280391 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280391' /scratch/stefan/7769901/working/building/REAL300000280391 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280391 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280391/0 /scratch/stefan/7769901/working/building/REAL300000280391 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/550 `/scratch/stefan/7769901/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-]) `REAL300000280391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280391 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 2, 2, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 38, 21, 22, 23, 24, 27, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280391 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 21, 22, 23, 24, 25, 26, 27, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280391 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280391/1 /scratch/stefan/7769901/working/building/REAL300000280391 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/551 `/scratch/stefan/7769901/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-]) `REAL300000280391.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280391 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 11, 11, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 2, 2, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 21, 22, 23, 24, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280391 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 11, 11, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280391 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280391 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280391/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280391/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280391 Building REAL300000280392 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280392' /scratch/stefan/7769901/working/building/REAL300000280392 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280392 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280392/0 /scratch/stefan/7769901/working/building/REAL300000280392 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/552 `/scratch/stefan/7769901/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280392 none O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1] 54 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 36] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280392 none O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 26, 10, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54] 54 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280392 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280392 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280392/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280392 Building REAL300000280393 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280393' /scratch/stefan/7769901/working/building/REAL300000280393 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280393 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280393/0 /scratch/stefan/7769901/working/building/REAL300000280393 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/553 `/scratch/stefan/7769901/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(C)=C1C(=O)[O-]) `REAL300000280393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280393 none CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 5, 1, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280393 none CC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 5, 1, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280393 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280393 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280393/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280393 Building REAL300000280394 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280394' /scratch/stefan/7769901/working/building/REAL300000280394 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280394 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280394/0 /scratch/stefan/7769901/working/building/REAL300000280394 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/554 `/scratch/stefan/7769901/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280394 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 75, 75, 75, 45, 75, 75, 75, 75, 75, 75, 1, 1, 1, 3, 3, 2, 2, 2, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280394 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75] 75 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280394 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280394/1 /scratch/stefan/7769901/working/building/REAL300000280394 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/555 `/scratch/stefan/7769901/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280394.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280394 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 66, 66, 66, 41, 66, 66, 66, 66, 66, 66, 1, 1, 1, 3, 3, 2, 2, 2, 1, 25, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280394 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 22, 8, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66] 66 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280394 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280394 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280394/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280394/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280394 Building REAL300000280395 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280395' /scratch/stefan/7769901/working/building/REAL300000280395 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280395 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280395/0 /scratch/stefan/7769901/working/building/REAL300000280395 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/556 `/scratch/stefan/7769901/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1Cl) `REAL300000280395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280395 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280395 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 9, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280395 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280395/1 /scratch/stefan/7769901/working/building/REAL300000280395 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/557 `/scratch/stefan/7769901/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1Cl) `REAL300000280395.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280395 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 1, 1, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280395 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280395 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280395 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280395/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280395/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280395 Building REAL300000280396 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280396' /scratch/stefan/7769901/working/building/REAL300000280396 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280396 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280396/0 /scratch/stefan/7769901/working/building/REAL300000280396 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/558 `/scratch/stefan/7769901/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280396 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 1, 7, 7, 7, 25, 97, 97, 97, 43, 97, 97, 97, 97, 97, 97, 1, 2, 2, 2, 1, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1] 97 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 39, 25, 29] set([5, 6, 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280396 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 97, 97, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280396 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280396 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280396/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280396 Building REAL300000280397 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280397' /scratch/stefan/7769901/working/building/REAL300000280397 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280397 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280397/0 /scratch/stefan/7769901/working/building/REAL300000280397 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/559 `/scratch/stefan/7769901/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280397 none CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 36 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 43, 21, 22, 23, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280397 none CCC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 23, 23, 36, 36, 36, 36, 36, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 36 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280397 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280397 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280397/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280397 Building REAL300000280398 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280398' /scratch/stefan/7769901/working/building/REAL300000280398 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280398 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280398/0 /scratch/stefan/7769901/working/building/REAL300000280398 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/560 `/scratch/stefan/7769901/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1CC(=O)[O-]) `REAL300000280398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280398 none COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 7, 7, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 3, 3] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 21, 22, 23, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280398 none COC1=CC=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 31, 37, 37, 32, 32, 32, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 31, 31] 37 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280398 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280398 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280398/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280398 Building REAL300000280399 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280399' /scratch/stefan/7769901/working/building/REAL300000280399 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280399 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280399/0 /scratch/stefan/7769901/working/building/REAL300000280399 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/561 `/scratch/stefan/7769901/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280399 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280399 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280399 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280399/1 /scratch/stefan/7769901/working/building/REAL300000280399 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/562 `/scratch/stefan/7769901/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280399.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280399 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280399 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 11, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280399 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280399 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280399/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280399/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280399 Building REAL300000280400 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280400' /scratch/stefan/7769901/working/building/REAL300000280400 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280400 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280400/0 /scratch/stefan/7769901/working/building/REAL300000280400 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/563 `/scratch/stefan/7769901/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl) `REAL300000280400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280400 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 40, 19, 20, 21, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280400 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 40, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280400 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280400/1 /scratch/stefan/7769901/working/building/REAL300000280400 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/564 `/scratch/stefan/7769901/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl) `REAL300000280400.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280400 none CC1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 20, 20, 20, 16, 20, 20, 20, 20, 20, 20, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 39, 19, 20, 21, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280400 none CC1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280400 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280400 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280400/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280400/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280400 Building REAL300000280401 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280401' /scratch/stefan/7769901/working/building/REAL300000280401 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280401 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280401/0 /scratch/stefan/7769901/working/building/REAL300000280401 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/565 `/scratch/stefan/7769901/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280401 none CCN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 41, 41, 28, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 59 rigid atoms, others: [1, 2, 3, 4, 5, 41, 20, 21, 22, 23, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280401 none CCN1C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 41, 41, 23, 9, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 59, 59, 59, 59, 59, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 41, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280401 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280401/1 /scratch/stefan/7769901/working/building/REAL300000280401 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/566 `/scratch/stefan/7769901/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280401.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280401 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 41, 41, 41, 40, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 60 rigid atoms, others: [1, 2, 3, 4, 5, 40, 20, 21, 22, 23, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280401 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 41, 41, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 60, 60, 60, 60, 60, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 60 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 40, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280401 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280401 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280401/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280401/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280401 Building REAL300000280402 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280402' /scratch/stefan/7769901/working/building/REAL300000280402 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280402 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280402/0 /scratch/stefan/7769901/working/building/REAL300000280402 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/567 `/scratch/stefan/7769901/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280402 none CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 26, 26, 26, 16, 26, 26, 26, 26, 26, 26, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280402 none CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280402 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280402/1 /scratch/stefan/7769901/working/building/REAL300000280402 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/568 `/scratch/stefan/7769901/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280402.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280402 none CC1=C(Cl)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 30, 30, 16, 30, 30, 30, 30, 30, 30, 1, 1, 1, 3, 3, 2, 2, 2, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280402 none CC1=C(Cl)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 9, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 30 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280402 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280402 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280402/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280402/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280402 Building REAL300000280403 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280403' /scratch/stefan/7769901/working/building/REAL300000280403 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280403 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280403/0 /scratch/stefan/7769901/working/building/REAL300000280403 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/569 `/scratch/stefan/7769901/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1C(=O)[O-]) `REAL300000280403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280403 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 45, 45, 45, 17, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 19, 20, 21, 22, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280403 none CC1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 23, 9, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280403 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280403 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280403/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280403 Building REAL300000280404 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280404' /scratch/stefan/7769901/working/building/REAL300000280404 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280404 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280404/0 /scratch/stefan/7769901/working/building/REAL300000280404 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/570 `/scratch/stefan/7769901/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280404 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 5, 5, 5, 12, 40, 40, 40, 37, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 29, 30] set([7, 8, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280404 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 9, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280404 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280404 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280404/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280404 Building REAL300000280405 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280405' /scratch/stefan/7769901/working/building/REAL300000280405 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280405 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280405/0 /scratch/stefan/7769901/working/building/REAL300000280405 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/571 `/scratch/stefan/7769901/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1[N+](=O)[O-]) `REAL300000280405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280405 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280405 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 9, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280405 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280405 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280405/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280405 Building REAL300000280406 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280406' /scratch/stefan/7769901/working/building/REAL300000280406 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280406 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280406/0 /scratch/stefan/7769901/working/building/REAL300000280406 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/572 `/scratch/stefan/7769901/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F) `REAL300000280406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280406 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 78, 78, 78, 48, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280406 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 78, 32, 11, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280406 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280406 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280406/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280406 Building REAL300000280407 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280407' /scratch/stefan/7769901/working/building/REAL300000280407 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280407 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280407/0 /scratch/stefan/7769901/working/building/REAL300000280407 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/573 `/scratch/stefan/7769901/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280407 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 26, 26, 26, 16, 26, 26, 26, 26, 26, 26, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280407 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280407 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280407/1 /scratch/stefan/7769901/working/building/REAL300000280407 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/574 `/scratch/stefan/7769901/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-]) `REAL300000280407.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280407 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 16, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 2, 2, 2, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280407 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280407 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280407 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280407/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280407/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280407 Building REAL300000280408 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280408' /scratch/stefan/7769901/working/building/REAL300000280408 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280408 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280408/0 /scratch/stefan/7769901/working/building/REAL300000280408 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/575 `/scratch/stefan/7769901/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21) `REAL300000280408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280408 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 19, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 41, 42, 43, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280408 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280408 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280408/1 /scratch/stefan/7769901/working/building/REAL300000280408 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/576 `/scratch/stefan/7769901/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21) `REAL300000280408.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280408 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 41, 42, 40, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280408 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280408 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280408 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280408/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280408/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280408 Building REAL300000280409 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280409' /scratch/stefan/7769901/working/building/REAL300000280409 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280409 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280409/0 /scratch/stefan/7769901/working/building/REAL300000280409 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/577 `/scratch/stefan/7769901/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1) `REAL300000280409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280409 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 24, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280409 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280409 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280409 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280409/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280409 Building REAL300000280410 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280410' /scratch/stefan/7769901/working/building/REAL300000280410 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280410 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280410/0 /scratch/stefan/7769901/working/building/REAL300000280410 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/578 `/scratch/stefan/7769901/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1) `REAL300000280410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280410 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 66, 66, 66, 44, 66, 66, 66, 66, 66, 66, 4, 4, 4, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66] 66 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280410 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 52, 66, 66, 66, 66, 66, 29, 10, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280410 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280410/1 /scratch/stefan/7769901/working/building/REAL300000280410 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/579 `/scratch/stefan/7769901/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1) `REAL300000280410.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280410 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 23, 46, 46, 46, 42, 46, 46, 46, 46, 46, 46, 4, 4, 4, 1, 1, 1, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 29, 30, 31] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280410 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 39, 46, 46, 46, 46, 46, 24, 11, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280410 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280410 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280410/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280410/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280410 Building REAL300000280411 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280411' /scratch/stefan/7769901/working/building/REAL300000280411 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280411 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280411/0 /scratch/stefan/7769901/working/building/REAL300000280411 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/580 `/scratch/stefan/7769901/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C(Cl)O1) `REAL300000280411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280411 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 22, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [1, 3, 4, 5, 6, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280411 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 26, 10, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280411 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280411 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280411/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280411 Building REAL300000280412 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280412' /scratch/stefan/7769901/working/building/REAL300000280412 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280412 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280412/0 /scratch/stefan/7769901/working/building/REAL300000280412 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/581 `/scratch/stefan/7769901/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2)CC1) `REAL300000280412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 33, 19, 33, 33, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 38, 38, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 38, 38, 38, 38] 38 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 7, 7, 6, 6, 8, 8, 8, 15, 38, 38, 38, 23, 38, 38, 38, 38, 38, 38, 7, 7, 1, 1, 7, 7, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 1, 1, 1, 1] 38 rigid atoms, others: [1, 3, 4, 41, 42, 43, 44, 25, 26] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 17, 33, 33, 33, 33, 33, 33, 1, 1, 7, 7, 1, 1, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 7, 7, 7, 7] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 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, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280412 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280412/1 /scratch/stefan/7769901/working/building/REAL300000280412 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/582 `/scratch/stefan/7769901/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2)CC1) `REAL300000280412.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 21, 39, 39, 21, 9, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 49, 49, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 49, 49, 49, 49] 49 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 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, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 7, 7, 5, 6, 10, 10, 10, 20, 49, 49, 49, 28, 49, 49, 49, 49, 49, 49, 7, 7, 1, 1, 7, 7, 49, 49, 49, 49, 49, 49, 49, 49, 49, 7, 7, 1, 1, 1, 1] 49 rigid atoms, others: [1, 3, 4, 40, 41, 42, 43, 25, 26] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280412 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 7, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 39, 39, 39, 17, 39, 39, 39, 39, 39, 39, 1, 1, 7, 7, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 7, 7, 7, 7] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 39, 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, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280412 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280412 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280412/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280412/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280412 Building REAL300000280413 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280413' /scratch/stefan/7769901/working/building/REAL300000280413 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280413 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280413/0 /scratch/stefan/7769901/working/building/REAL300000280413 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/583 `/scratch/stefan/7769901/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2C1) `REAL300000280413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280413 none O=C([O-])C1CC2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1] 22 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 42, 43, 44, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280413 none O=C([O-])C1CC2=CC=C(S(=O)(=O)NC3=CC=C4OCCCOC4=C3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22] 22 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280413 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280413/1 /scratch/stefan/7769901/working/building/REAL300000280413 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/584 `/scratch/stefan/7769901/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2C1) `REAL300000280413.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280413 none O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 27, 17, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 42, 43, 41, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280413 none O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C4OCCCOC4=C3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280413 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280413 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280413/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280413/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280413 Building REAL300000280414 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280414' /scratch/stefan/7769901/working/building/REAL300000280414 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280414 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280414/0 /scratch/stefan/7769901/working/building/REAL300000280414 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/585 `/scratch/stefan/7769901/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1) `REAL300000280414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280414 none CCC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 21, 80, 80, 80, 42, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1] 89 rigid atoms, others: [1, 2, 3, 4, 39, 19, 20, 21, 22, 23, 24] set([0, 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: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280414 none CCC1=C(S(=O)(=O)[N-]C2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 80, 80, 31, 11, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 89 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 222 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280414 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280414/1 /scratch/stefan/7769901/working/building/REAL300000280414 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/586 `/scratch/stefan/7769901/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1) `REAL300000280414.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280414 none CCC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 5, 5, 5, 13, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 60 rigid atoms, others: [1, 2, 3, 4, 40, 19, 20, 21, 22, 23, 24] set([0, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280414 none CCC1=C(S(=O)(=O)NC2=CC=C3OCCCOC3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 57, 57, 29, 10, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 60, 60, 60, 60, 60, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 60 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 40, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280414 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280414 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280414/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280414/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280414 Building REAL300000280415 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280415' /scratch/stefan/7769901/working/building/REAL300000280415 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280415 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280415/0 /scratch/stefan/7769901/working/building/REAL300000280415 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/587 `/scratch/stefan/7769901/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F) `REAL300000280415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 26, 27, 28, 29]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 24, 25, 26, 27, 28] set([0, 2, 7, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 26, 27, 28, 29]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280415 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280415/1 /scratch/stefan/7769901/working/building/REAL300000280415 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/588 `/scratch/stefan/7769901/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F) `REAL300000280415.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 24, 25, 26, 27, 28]) total number of confs: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 39, 27, 24, 25, 26, 38, 28] set([0, 2, 7, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280415 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 24, 25, 26, 27, 28]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280415 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280415 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280415/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280415/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280415 Building REAL300000280416 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280416' /scratch/stefan/7769901/working/building/REAL300000280416 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280416 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280416/0 /scratch/stefan/7769901/working/building/REAL300000280416 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/589 `/scratch/stefan/7769901/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1) `REAL300000280416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280416 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280416/1 /scratch/stefan/7769901/working/building/REAL300000280416 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/590 `/scratch/stefan/7769901/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1) `REAL300000280416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 39, 38, 25, 26, 27, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280416 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280416 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280416 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280416/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280416/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280416 Building REAL300000280417 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280417' /scratch/stefan/7769901/working/building/REAL300000280417 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280417 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280417/0 /scratch/stefan/7769901/working/building/REAL300000280417 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/591 `/scratch/stefan/7769901/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 26, 27, 28, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 26, 27, 28, 29] set([9, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 26, 27, 28, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280417 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280417/1 /scratch/stefan/7769901/working/building/REAL300000280417 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/592 `/scratch/stefan/7769901/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280417.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([9, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280417 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280417 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280417 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280417/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280417/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280417 Building REAL300000280418 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280418' /scratch/stefan/7769901/working/building/REAL300000280418 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280418 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280418/0 /scratch/stefan/7769901/working/building/REAL300000280418 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/593 `/scratch/stefan/7769901/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 23, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280418 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280418/1 /scratch/stefan/7769901/working/building/REAL300000280418 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/594 `/scratch/stefan/7769901/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280418.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 42, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 42, 23, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280418 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 42, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280418 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280418 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280418/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280418/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280418 Building REAL300000280419 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280419' /scratch/stefan/7769901/working/building/REAL300000280419 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280419 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280419/0 /scratch/stefan/7769901/working/building/REAL300000280419 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/595 `/scratch/stefan/7769901/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280419 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87] 87 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 27, 28, 29]) total number of confs: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280419 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280419 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87] 87 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 27, 28, 29]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280419 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280419 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280419/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280419 Building REAL300000280420 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280420' /scratch/stefan/7769901/working/building/REAL300000280420 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280420 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280420/0 /scratch/stefan/7769901/working/building/REAL300000280420 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/596 `/scratch/stefan/7769901/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280420 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83] 83 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280420 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280420 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83] 83 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280420 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280420 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280420/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280420 Building REAL300000280421 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280421' /scratch/stefan/7769901/working/building/REAL300000280421 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280421 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280421/0 /scratch/stefan/7769901/working/building/REAL300000280421 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/597 `/scratch/stefan/7769901/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1) `REAL300000280421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 45, 45, 45, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 8, 9, 10, 33, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 45, 45, 45, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280421 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280421/1 /scratch/stefan/7769901/working/building/REAL300000280421 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/598 `/scratch/stefan/7769901/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=C2)=C1) `REAL300000280421.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 69, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 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, 2, 2, 1, 1, 1, 7, 7, 7, 15, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 8, 9, 10, 33, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280421 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 69, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280421 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280421 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280421/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280421/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280421 Building REAL300000280422 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280422' /scratch/stefan/7769901/working/building/REAL300000280422 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280422 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280422/0 /scratch/stefan/7769901/working/building/REAL300000280422 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/599 `/scratch/stefan/7769901/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 40, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 172 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 2, 2, 2, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 40, 22, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 40, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280422 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280422/1 /scratch/stefan/7769901/working/building/REAL300000280422 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/600 `/scratch/stefan/7769901/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280422.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 2, 2, 2, 2, 2, 1, 9, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 41, 22, 23, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280422 none CN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280422 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280422 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280422/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280422/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280422 Building REAL300000280423 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280423' /scratch/stefan/7769901/working/building/REAL300000280423 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280423 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280423/0 /scratch/stefan/7769901/working/building/REAL300000280423 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/601 `/scratch/stefan/7769901/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280423 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 26, 27, 28, 29]) total number of confs: 187 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280423 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 20, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 2, 2, 2, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1] 80 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 39, 26] set([4, 5, 9, 10, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280423 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 26, 27, 28, 29]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280423 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280423 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280423/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280423 Building REAL300000280424 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280424' /scratch/stefan/7769901/working/building/REAL300000280424 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280424 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280424/0 /scratch/stefan/7769901/working/building/REAL300000280424 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/602 `/scratch/stefan/7769901/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1) `REAL300000280424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 24, 25, 26, 36] set([0, 2, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280424 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280424/1 /scratch/stefan/7769901/working/building/REAL300000280424 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/603 `/scratch/stefan/7769901/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1) `REAL300000280424.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 55 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 24, 25, 26, 37] set([0, 2, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280424 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 55 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280424 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280424 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280424/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280424/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280424 Building REAL300000280425 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280425' /scratch/stefan/7769901/working/building/REAL300000280425 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280425 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280425/0 /scratch/stefan/7769901/working/building/REAL300000280425 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/604 `/scratch/stefan/7769901/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1) `REAL300000280425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69] 69 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 178 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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] 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, 7, 7, 7, 17, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 2, 2, 2, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1] 69 rigid atoms, others: [0, 1, 2, 3, 39, 21, 22, 23, 24, 25, 26] set([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, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69] 69 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280425 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280425/1 /scratch/stefan/7769901/working/building/REAL300000280425 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/605 `/scratch/stefan/7769901/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1) `REAL300000280425.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 49 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1] 49 rigid atoms, others: [0, 1, 2, 3, 40, 21, 22, 23, 24, 25, 26] set([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, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280425 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 49 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280425 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280425 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280425/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280425/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280425 Building REAL300000280426 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280426' /scratch/stefan/7769901/working/building/REAL300000280426 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280426 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280426/0 /scratch/stefan/7769901/working/building/REAL300000280426 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/606 `/scratch/stefan/7769901/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1) `REAL300000280426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 156 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 2, 2, 2, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 39, 21, 22, 23, 24, 25, 26] set([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, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280426 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280426/1 /scratch/stefan/7769901/working/building/REAL300000280426 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/607 `/scratch/stefan/7769901/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1) `REAL300000280426.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 40, 21, 22, 23, 24, 25, 26] set([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, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280426 none CC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280426 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280426 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280426/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280426/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280426 Building REAL300000280427 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280427' /scratch/stefan/7769901/working/building/REAL300000280427 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280427 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280427/0 /scratch/stefan/7769901/working/building/REAL300000280427 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/608 `/scratch/stefan/7769901/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F) `REAL300000280427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 25, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280427 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280427/1 /scratch/stefan/7769901/working/building/REAL300000280427 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/609 `/scratch/stefan/7769901/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F) `REAL300000280427.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27, 28, 29]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 25, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280427 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27, 28, 29]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280427 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280427 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280427/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280427/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280427 Building REAL300000280428 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280428' /scratch/stefan/7769901/working/building/REAL300000280428 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280428 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280428/0 /scratch/stefan/7769901/working/building/REAL300000280428 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/610 `/scratch/stefan/7769901/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)S1) `REAL300000280428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280428 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280428 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 17, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65] 65 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280428 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280428 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280428 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280428/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280428 Building REAL300000280429 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280429' /scratch/stefan/7769901/working/building/REAL300000280429 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280429 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280429/0 /scratch/stefan/7769901/working/building/REAL300000280429 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/611 `/scratch/stefan/7769901/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 27, 28, 29] set([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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280429 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280429/1 /scratch/stefan/7769901/working/building/REAL300000280429 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/612 `/scratch/stefan/7769901/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280429.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 27, 28, 29] set([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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280429 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280429 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280429 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280429/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280429/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280429 Building REAL300000280430 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280430' /scratch/stefan/7769901/working/building/REAL300000280430 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280430 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280430/0 /scratch/stefan/7769901/working/building/REAL300000280430 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/613 `/scratch/stefan/7769901/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C(F)=C1) `REAL300000280430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280430 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280430 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280430 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280430 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280430 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280430/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280430 Building REAL300000280431 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280431' /scratch/stefan/7769901/working/building/REAL300000280431 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280431 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280431/0 /scratch/stefan/7769901/working/building/REAL300000280431 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/614 `/scratch/stefan/7769901/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 84, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 168, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84] 168 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 363 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 2, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1] 168 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 40, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 84, 35, 11, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 168, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84] 168 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280431 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280431/1 /scratch/stefan/7769901/working/building/REAL300000280431 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/615 `/scratch/stefan/7769901/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280431.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 40, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280431 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280431 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280431 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280431/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280431/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280431 Building REAL300000280432 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280432' /scratch/stefan/7769901/working/building/REAL300000280432 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280432 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280432/0 /scratch/stefan/7769901/working/building/REAL300000280432 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/616 `/scratch/stefan/7769901/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1) `REAL300000280432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 47, 47, 27, 9, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 42, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 3, 3, 3, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 42, 43, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 47, 47, 27, 9, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 42, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280432 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280432/1 /scratch/stefan/7769901/working/building/REAL300000280432 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/617 `/scratch/stefan/7769901/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1) `REAL300000280432.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 29, 29, 55, 55, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 42, 41, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 2, 2, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 26, 27, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280432 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 29, 29, 55, 55, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 42, 41, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280432 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280432 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280432/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280432/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280432 Building REAL300000280433 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280433' /scratch/stefan/7769901/working/building/REAL300000280433 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280433 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280433/0 /scratch/stefan/7769901/working/building/REAL300000280433 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/618 `/scratch/stefan/7769901/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1) `REAL300000280433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280433 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280433/1 /scratch/stefan/7769901/working/building/REAL300000280433 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/619 `/scratch/stefan/7769901/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=C2)=C1) `REAL300000280433.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 62, 62, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 15, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62] 62 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280433 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=CC(C#CC2=CC=CC=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', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 62, 62, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280433 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280433 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280433/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280433/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280433 Building REAL300000280434 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280434' /scratch/stefan/7769901/working/building/REAL300000280434 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280434 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280434/0 /scratch/stefan/7769901/working/building/REAL300000280434 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/620 `/scratch/stefan/7769901/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1) `REAL300000280434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280434 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 33, 41, 41, 41, 41, 41, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280434 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280434 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=CC(C#CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 33, 41, 41, 41, 41, 41, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280434 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280434 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280434/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280434 Building REAL300000280435 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280435' /scratch/stefan/7769901/working/building/REAL300000280435 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280435 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280435/0 /scratch/stefan/7769901/working/building/REAL300000280435 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/621 `/scratch/stefan/7769901/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 119, 119, 119, 119, 119, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 119 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 496 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 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: [3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1] 119 rigid atoms, others: [1, 2, 3, 4, 5, 33, 43, 23, 24, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 65, 65, 65, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 119, 119, 119, 119, 119, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65] 119 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280435 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280435/1 /scratch/stefan/7769901/working/building/REAL300000280435 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/622 `/scratch/stefan/7769901/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-]) `REAL300000280435.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 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] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 63, 63, 63, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 113, 113, 113, 113, 113, 63, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63] 113 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 44, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 479 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 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] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1] 113 rigid atoms, others: [1, 2, 3, 4, 5, 33, 44, 23, 24, 25, 26, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280435 none CCN1C=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 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] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 63, 63, 63, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 113, 113, 113, 113, 113, 63, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63] 113 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 44, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280435 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280435 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280435/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280435/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280435 Building REAL300000280436 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280436' /scratch/stefan/7769901/working/building/REAL300000280436 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280436 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280436/0 /scratch/stefan/7769901/working/building/REAL300000280436 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/623 `/scratch/stefan/7769901/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-]) `REAL300000280436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 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] 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 43, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 151 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 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] 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, 3, 3, 3, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 22, 23, 24, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 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] 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 43, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280436 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280436/1 /scratch/stefan/7769901/working/building/REAL300000280436 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/624 `/scratch/stefan/7769901/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-]) `REAL300000280436.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 22, 23, 24, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280436 none CC1=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280436 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280436 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280436/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280436/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280436 Building REAL300000280437 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280437' /scratch/stefan/7769901/working/building/REAL300000280437 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280437 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280437/0 /scratch/stefan/7769901/working/building/REAL300000280437 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/625 `/scratch/stefan/7769901/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1F) `REAL300000280437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280437 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30]) total number of confs: 203 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280437 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100, 100, 100] 100 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280437 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280437 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280437 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280437/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280437 Building REAL300000280438 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280438' /scratch/stefan/7769901/working/building/REAL300000280438 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280438 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280438/0 /scratch/stefan/7769901/working/building/REAL300000280438 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/626 `/scratch/stefan/7769901/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1) `REAL300000280438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280438 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 37, 13, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111] 111 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 26, 27, 28]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280438 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 5, 5, 5, 17, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28] set([9, 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280438 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 37, 13, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111] 111 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 26, 27, 28]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280438 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280438 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280438/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280438 Building REAL300000280439 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280439' /scratch/stefan/7769901/working/building/REAL300000280439 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280439 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280439/0 /scratch/stefan/7769901/working/building/REAL300000280439 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/627 `/scratch/stefan/7769901/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1) `REAL300000280439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102] 102 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 23, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1] 102 rigid atoms, others: [1, 2, 3, 4, 42, 22, 23, 24, 25, 26, 27] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)[N-]C2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 37, 12, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102] 102 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280439 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280439/1 /scratch/stefan/7769901/working/building/REAL300000280439 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/628 `/scratch/stefan/7769901/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1) `REAL300000280439.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 32, 43, 33, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 195 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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: [6, 1, 1, 1, 1, 5, 5, 5, 13, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1] 80 rigid atoms, others: [1, 2, 3, 4, 43, 22, 23, 24, 25, 26, 27] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280439 none CCC1=C(S(=O)(=O)NC2=CC=CC(C#CC3=CC=CC=C3)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 32, 43, 33, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280439 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280439 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280439/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280439/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280439 Building REAL300000280440 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280440' /scratch/stefan/7769901/working/building/REAL300000280440 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280440 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280440/0 /scratch/stefan/7769901/working/building/REAL300000280440 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/629 `/scratch/stefan/7769901/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280440 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 85, 85, 13, 13, 1, 1, 13, 13, 1, 1, 7, 13, 13, 49, 49, 49, 13, 13, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 318 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280440 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 5, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 13, 13, 73, 73, 13, 13, 5, 1, 1, 5, 5, 5, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 37, 38, 9, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40]) total number of confs: 309 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280440 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280440/1 /scratch/stefan/7769901/working/building/REAL300000280440 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/630 `/scratch/stefan/7769901/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280440.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280440 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 20, 76, 76, 76, 76, 119, 119, 20, 20, 1, 1, 13, 13, 1, 1, 20, 20, 76, 76, 76, 20, 20, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 25, 26, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 412 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280440 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 9, 9, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 1, 1, 20, 20, 70, 70, 20, 20, 1, 1, 7, 7, 7, 1, 1, 20, 20] 201 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 299 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280440 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280440 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280440/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280440/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280440 Building REAL300000280441 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280441' /scratch/stefan/7769901/working/building/REAL300000280441 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280441 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280441/0 /scratch/stefan/7769901/working/building/REAL300000280441 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/631 `/scratch/stefan/7769901/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280441 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 3, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 67, 67, 41, 1, 1, 13, 13, 1, 1, 9, 41, 41, 41, 1, 1] 149 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 258 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280441 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 67, 9, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 149, 149, 41, 41, 9, 1, 1, 1, 41, 41] 149 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 600 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280441 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280441 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280441/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280441 Building REAL300000280442 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280442' /scratch/stefan/7769901/working/building/REAL300000280442 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280442 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280442/0 /scratch/stefan/7769901/working/building/REAL300000280442 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/632 `/scratch/stefan/7769901/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280442 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 22, 82, 140, 140, 29, 29, 4, 4, 4, 1, 1, 5, 5, 1, 29, 29, 140, 140, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 34, 13, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 539 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280442 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 80, 80, 120, 120, 29, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 6, 25, 25, 1, 1, 48, 48, 48, 29, 29, 80, 80, 29, 1, 1, 25, 25, 1, 1] 201 rigid atoms, others: [35, 36, 39, 40, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 465 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280442 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280442/1 /scratch/stefan/7769901/working/building/REAL300000280442 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/633 `/scratch/stefan/7769901/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280442.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280442 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 23, 86, 122, 122, 29, 29, 4, 4, 4, 1, 1, 5, 5, 1, 17, 29, 29, 122, 122, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 34, 13, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280442 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [39, 29, 29, 29, 29, 29, 29, 92, 92, 135, 135, 29, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 5, 17, 17, 1, 1, 39, 39, 39, 29, 29, 92, 92, 29, 4, 1, 1, 17, 17, 1, 1] 201 rigid atoms, others: [36, 37, 40, 41, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 464 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280442 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280442 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280442/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280442/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280442 Building REAL300000280443 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280443' /scratch/stefan/7769901/working/building/REAL300000280443 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280443 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280443/0 /scratch/stefan/7769901/working/building/REAL300000280443 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/634 `/scratch/stefan/7769901/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000280443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280443 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 11, 11, 1, 1, 7, 15, 15, 15, 15, 1, 1] 53 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 84 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280443 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 25, 5, 5, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 53, 53, 15, 15, 5, 1, 1, 1, 1, 15, 15] 53 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 203 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280443 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280443 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280443/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280443 Building REAL300000280444 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280444' /scratch/stefan/7769901/working/building/REAL300000280444 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280444 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280444/0 /scratch/stefan/7769901/working/building/REAL300000280444 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/635 `/scratch/stefan/7769901/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000280444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280444 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 3, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 14, 14, 1, 1, 9, 27, 27, 27, 27, 1, 1] 95 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 120 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280444 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 95, 51, 9, 9, 27, 27, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 95, 95, 27, 27, 9, 1, 1, 1, 1, 27, 27] 95 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 371 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280444 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280444 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280444/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280444 Building REAL300000280445 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280445' /scratch/stefan/7769901/working/building/REAL300000280445 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280445 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280445/0 /scratch/stefan/7769901/working/building/REAL300000280445 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/636 `/scratch/stefan/7769901/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280445 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 49, 49, 23, 34, 142, 201, 201, 49, 49, 4, 4, 4, 1, 1, 1, 49, 49, 201, 200, 49, 49] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 650 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280445 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 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: [90, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 25, 25, 1, 1, 90, 90, 90, 49, 49, 49, 1, 1, 26, 26, 1, 1] 201 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 254 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280445 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280445/1 /scratch/stefan/7769901/working/building/REAL300000280445 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/637 `/scratch/stefan/7769901/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280445.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280445 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 53, 53, 24, 41, 137, 201, 201, 53, 53, 4, 4, 4, 1, 1, 1, 24, 53, 53, 201, 201, 53, 53] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 680 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280445 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [77, 53, 53, 53, 53, 53, 53, 53, 53, 53, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 27, 27, 1, 1, 77, 77, 77, 53, 53, 53, 6, 1, 1, 27, 27, 1, 1] 201 rigid atoms, others: [32, 33, 36, 37, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 234 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280445 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280445 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280445/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280445/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280445 Building REAL300000280446 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280446' /scratch/stefan/7769901/working/building/REAL300000280446 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280446 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280446/0 /scratch/stefan/7769901/working/building/REAL300000280446 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/638 `/scratch/stefan/7769901/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1) `REAL300000280446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280446 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 3, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 21, 21, 21, 65, 65, 108, 108, 21, 21, 1, 1, 15, 15, 1, 1, 8, 21, 21, 65, 65, 21, 21, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 401 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280446 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 35, 5, 5, 21, 21, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 19, 19, 1, 1, 21, 21, 119, 119, 21, 21, 5, 1, 1, 5, 5, 1, 1, 21, 21] 201 rigid atoms, others: [34, 35, 9, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 487 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280446 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280446 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280446/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280446 Building REAL300000280447 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280447' /scratch/stefan/7769901/working/building/REAL300000280447 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280447 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280447/0 /scratch/stefan/7769901/working/building/REAL300000280447 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/639 `/scratch/stefan/7769901/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280447 none CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 16, 63, 126, 126, 21, 21, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 21, 21, 126, 126, 21, 21, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 36, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 477 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280447 none CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 21, 21, 21, 33, 33, 21, 21, 21, 21, 21, 6, 1, 1, 24, 24, 1, 1, 21] 126 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 179 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280447 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280447 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280447/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280447 Building REAL300000280448 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280448' /scratch/stefan/7769901/working/building/REAL300000280448 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280448 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280448/0 /scratch/stefan/7769901/working/building/REAL300000280448 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/640 `/scratch/stefan/7769901/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1) `REAL300000280448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280448 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 14, 14, 1, 1, 42, 42, 42, 1, 1] 70 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 160 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280448 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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, 48, 13, 13, 42, 42, 13, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 42, 42, 70, 70, 42, 42, 1, 1, 1, 42, 42] 70 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 263 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280448 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280448/1 /scratch/stefan/7769901/working/building/REAL300000280448 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/641 `/scratch/stefan/7769901/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1) `REAL300000280448.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280448 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 14, 14, 1, 1, 11, 47, 47, 47, 1, 1] 89 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280448 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 55, 27, 24, 47, 47, 17, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 47, 47, 89, 89, 47, 47, 17, 1, 1, 1, 47, 47] 89 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 339 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280448 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280448 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280448/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280448/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280448 Building REAL300000280449 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280449' /scratch/stefan/7769901/working/building/REAL300000280449 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280449 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280449/0 /scratch/stefan/7769901/working/building/REAL300000280449 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/642 `/scratch/stefan/7769901/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000280449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280449 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 27, 27, 27, 27, 27, 27, 41, 41, 27, 1, 1, 11, 11, 1, 1, 9, 27, 27, 27, 1, 1] 91 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280449 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 51, 9, 9, 27, 27, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 91, 91, 27, 27, 9, 1, 1, 1, 27, 27] 91 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 370 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280449 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280449 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280449/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280449 Building REAL300000280450 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280450' /scratch/stefan/7769901/working/building/REAL300000280450 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280450 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280450/0 /scratch/stefan/7769901/working/building/REAL300000280450 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/643 `/scratch/stefan/7769901/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1C) `REAL300000280450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280450 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 1, 3, 3, 3, 5, 17, 17, 5, 5, 32, 59, 59, 17, 17, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 59, 59, 17, 17, 2, 2, 2] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280450 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 23, 23, 1, 1, 17, 17, 17] 59 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280450 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280450 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280450/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280450 Building REAL300000280451 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280451' /scratch/stefan/7769901/working/building/REAL300000280451 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280451 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280451/0 /scratch/stefan/7769901/working/building/REAL300000280451 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/644 `/scratch/stefan/7769901/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1) `REAL300000280451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280451 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 14, 14, 1, 1, 90, 90, 90, 1, 1] 173 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 223 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280451 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [173, 173, 113, 25, 25, 90, 90, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 90, 90, 173, 173, 90, 90, 1, 1, 1, 90, 90] 173 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 673 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280451 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280451/1 /scratch/stefan/7769901/working/building/REAL300000280451 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/645 `/scratch/stefan/7769901/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1) `REAL300000280451.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280451 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 18, 18, 1, 1, 11, 101, 101, 101, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 255 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280451 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 25, 25, 101, 101, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 101, 101, 201, 201, 101, 101, 25, 1, 1, 1, 101, 101] 201 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 761 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280451 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280451 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280451/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280451/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280451 Building REAL300000280452 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280452' /scratch/stefan/7769901/working/building/REAL300000280452 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280452 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280452/0 /scratch/stefan/7769901/working/building/REAL300000280452 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/646 `/scratch/stefan/7769901/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1) `REAL300000280452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280452 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 31, 57, 66, 66, 13, 13, 1, 1, 11, 11, 1, 1, 7, 13, 13, 31, 31, 57, 57, 13, 13, 1, 1] 119 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 39, 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]) total number of confs: 324 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280452 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 49, 25, 7, 5, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 12, 17, 17, 1, 1, 13, 13, 49, 49, 13, 13, 5, 1, 1, 6, 6, 12, 12, 1, 1, 13, 13] 119 rigid atoms, others: [36, 37, 9, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39]) total number of confs: 251 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280452 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280452 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280452/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280452 Building REAL300000280453 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280453' /scratch/stefan/7769901/working/building/REAL300000280453 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280453 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280453/0 /scratch/stefan/7769901/working/building/REAL300000280453 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/647 `/scratch/stefan/7769901/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1) `REAL300000280453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280453 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [16, 16, 4, 1, 1, 1, 1, 1, 1, 11, 35, 35, 35, 95, 95, 95, 95, 95, 95, 95, 1, 1, 16, 16, 1, 1, 95, 95, 1, 1] 185 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27]) total number of confs: 243 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280453 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [183, 183, 121, 25, 25, 95, 95, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 183, 183, 95, 95, 1, 1, 95, 95] 185 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 706 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280453 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280453 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280453/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280453 Building REAL300000280454 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280454' /scratch/stefan/7769901/working/building/REAL300000280454 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280454 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280454/0 /scratch/stefan/7769901/working/building/REAL300000280454 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/648 `/scratch/stefan/7769901/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280454 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 25, 69, 95, 95, 31, 31, 2, 2, 2, 1, 1, 1, 13, 31, 31, 95, 95, 31, 31] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 326 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280454 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 31, 31, 31, 31, 31, 31, 6, 1, 1, 22, 22, 1, 1] 95 rigid atoms, others: [32, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 151 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280454 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280454 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280454/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280454 Building REAL300000280455 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280455' /scratch/stefan/7769901/working/building/REAL300000280455 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280455 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280455/0 /scratch/stefan/7769901/working/building/REAL300000280455 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/649 `/scratch/stefan/7769901/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1) `REAL300000280455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280455 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 57, 124, 138, 138, 13, 13, 1, 1, 14, 14, 1, 1, 7, 13, 13, 124, 124, 13, 13, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] 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]) total number of confs: 520 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280455 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 5, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 26, 41, 41, 1, 1, 13, 13, 58, 58, 13, 13, 5, 1, 1, 26, 26, 1, 1, 13, 13] 201 rigid atoms, others: [34, 35, 9, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 350 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280455 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280455 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280455/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280455 Building REAL300000280456 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280456' /scratch/stefan/7769901/working/building/REAL300000280456 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280456 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280456/0 /scratch/stefan/7769901/working/building/REAL300000280456 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/650 `/scratch/stefan/7769901/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280456 none CN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 3, 3, 9, 27, 27, 9, 21, 65, 111, 111, 27, 27, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 27, 27, 111, 111, 27, 27, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 404 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280456 none CN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 5, 23, 23, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 23, 23, 1, 1, 27] 111 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 152 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280456 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280456/1 /scratch/stefan/7769901/working/building/REAL300000280456 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/651 `/scratch/stefan/7769901/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280456.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280456 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 9, 16, 70, 101, 101, 27, 27, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 101, 101, 27, 27, 1] 101 rigid atoms, others: [0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 344 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280456 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 5, 25, 25, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 25, 25, 1, 1, 27] 101 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 152 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280456 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280456 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280456/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280456/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280456 Building REAL300000280457 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280457' /scratch/stefan/7769901/working/building/REAL300000280457 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280457 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280457/0 /scratch/stefan/7769901/working/building/REAL300000280457 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/652 `/scratch/stefan/7769901/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000280457 0 /scratch/stefan/7769901/working/building/REAL300000280457 /scratch/stefan/7769901/working /scratch/stefan/7769901 `0' -> `0.failed' Finished preparing REAL300000280457 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Found failed protomers Marking REAL300000280457 as failed mkdir: created directory `/scratch/stefan/7769901/failed' `/scratch/stefan/7769901/working/building/REAL300000280457' -> `/scratch/stefan/7769901/failed/REAL300000280457' Building REAL300000280458 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280458' /scratch/stefan/7769901/working/building/REAL300000280458 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280458 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280458/0 /scratch/stefan/7769901/working/building/REAL300000280458 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/653 `/scratch/stefan/7769901/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1) `REAL300000280458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280458 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 25, 64, 64, 25, 25, 137, 192, 192, 64, 64, 1, 2, 2, 2, 64, 64, 192, 192, 64, 64, 1] 193 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 22] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 641 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280458 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 99, 99, 64, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 28, 28, 1, 1, 64, 64, 64, 64, 1, 1, 28, 28, 1, 1, 64] 193 rigid atoms, others: [11, 12, 13, 14, 15, 16, 20, 21, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 32, 22, 23, 24, 25, 28, 29]) total number of confs: 340 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280458 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280458 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280458/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280458 Building REAL300000280459 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280459' /scratch/stefan/7769901/working/building/REAL300000280459 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280459 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280459/0 /scratch/stefan/7769901/working/building/REAL300000280459 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/654 `/scratch/stefan/7769901/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000280459 0 /scratch/stefan/7769901/working/building/REAL300000280459 /scratch/stefan/7769901/working /scratch/stefan/7769901 `0' -> `0.failed' Finished preparing REAL300000280459 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Found failed protomers Marking REAL300000280459 as failed `/scratch/stefan/7769901/working/building/REAL300000280459' -> `/scratch/stefan/7769901/failed/REAL300000280459' Building REAL300000280460 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280460' /scratch/stefan/7769901/working/building/REAL300000280460 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280460 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280460/0 /scratch/stefan/7769901/working/building/REAL300000280460 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/655 `/scratch/stefan/7769901/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000280460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280460 none N#CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 4, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 16, 16, 1, 1, 11, 33, 33, 1, 1] 106 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28]) total number of confs: 133 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280460 none N#CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 17, 17, 33, 33, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 106, 106, 33, 33, 9, 1, 1, 33, 33] 106 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 401 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280460 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280460/1 /scratch/stefan/7769901/working/building/REAL300000280460 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/656 `/scratch/stefan/7769901/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000280460.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280460 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 1, 1, 14, 14, 1, 1, 32, 32, 1, 1] 80 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27]) total number of confs: 118 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280460 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 60, 20, 17, 32, 32, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 32, 32, 80, 80, 32, 32, 1, 1, 32, 32] 80 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 272 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280460 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280460 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280460/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280460/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280460 Building REAL300000280461 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280461' /scratch/stefan/7769901/working/building/REAL300000280461 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280461 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280461/0 /scratch/stefan/7769901/working/building/REAL300000280461 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/657 `/scratch/stefan/7769901/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1OC) `REAL300000280461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280461 none COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 15, 16, 53, 104, 104, 21, 21, 1, 1, 1, 3, 3, 1, 1, 2, 4, 4, 4, 1, 9, 21, 21, 104, 104, 21, 21, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 24, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 392 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280461 none COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 21, 21, 21, 31, 31, 21, 21, 35, 43, 43, 43, 21, 6, 1, 1, 23, 23, 1, 1, 21, 35, 35, 35] 201 rigid atoms, others: [32, 33, 36, 37, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41]) total number of confs: 230 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280461 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280461 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280461/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280461 Building REAL300000280462 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280462' /scratch/stefan/7769901/working/building/REAL300000280462 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280462 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280462/0 /scratch/stefan/7769901/working/building/REAL300000280462 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/658 `/scratch/stefan/7769901/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280462 none COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 15, 66, 137, 137, 21, 21, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 9, 21, 21, 137, 137, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 509 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280462 none COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 21, 21, 21, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 21, 21, 21, 37, 37, 41, 41, 41, 21, 21, 4, 1, 1, 22, 22, 1, 1, 21] 201 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 227 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280462 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280462 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280462/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280462 Building REAL300000280463 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280463' /scratch/stefan/7769901/working/building/REAL300000280463 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280463 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280463/0 /scratch/stefan/7769901/working/building/REAL300000280463 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/659 `/scratch/stefan/7769901/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCCC3)C=C1) `REAL300000280463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280463 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCCC3)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 12, 12, 1, 1, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 60 rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 43, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280463 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCCC3)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 43, 9, 9, 32, 32, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 60, 60, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 60 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 43, 42, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 234 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280463 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280463 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280463/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280463 Building REAL300000280464 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280464' /scratch/stefan/7769901/working/building/REAL300000280464 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280464 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280464/0 /scratch/stefan/7769901/working/building/REAL300000280464 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/660 `/scratch/stefan/7769901/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280464 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 2, 2, 1, 1, 1, 3, 3, 3, 5, 15, 15, 5, 13, 42, 63, 63, 15, 15, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 15, 15, 63, 63, 15, 15] 63 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 35, 7] set([0, 2, 8, 9, 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: 231 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280464 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 5, 20, 20, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 20, 20, 1, 1] 63 rigid atoms, others: [37, 38, 41, 42, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 117 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280464 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280464 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280464/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280464 Building REAL300000280465 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280465' /scratch/stefan/7769901/working/building/REAL300000280465 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280465 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280465/0 /scratch/stefan/7769901/working/building/REAL300000280465 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/661 `/scratch/stefan/7769901/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280465 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 35, 35, 13, 27, 97, 181, 181, 35, 35, 6, 6, 6, 6, 6, 1, 1, 1, 13, 35, 35, 181, 181, 35, 35] 182 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 666 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280465 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [73, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 28, 28, 1, 1, 73, 73, 73, 73, 73, 35, 35, 35, 6, 1, 1, 28, 28, 1, 1] 182 rigid atoms, others: [34, 35, 38, 39, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 366 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280465 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280465 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280465/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280465 Building REAL300000280466 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280466' /scratch/stefan/7769901/working/building/REAL300000280466 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280466 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280466/0 /scratch/stefan/7769901/working/building/REAL300000280466 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/662 `/scratch/stefan/7769901/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280466 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 15, 25, 25, 15, 19, 36, 52, 52, 25, 25, 4, 4, 4, 1, 1, 2, 2, 1, 25, 25, 52, 52, 25, 25] 54 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280466 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 25, 25, 25, 25, 25, 25, 31, 37, 37, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 6, 16, 16, 1, 1, 33, 33, 33, 25, 25, 31, 31, 25, 1, 1, 16, 16, 1, 1] 54 rigid atoms, others: [34, 35, 38, 39, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 173 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280466 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280466/1 /scratch/stefan/7769901/working/building/REAL300000280466 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/663 `/scratch/stefan/7769901/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280466.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280466 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 17, 27, 27, 21, 23, 44, 59, 59, 27, 27, 4, 4, 4, 1, 1, 2, 2, 1, 17, 27, 27, 59, 59, 27, 27] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 231 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280466 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [33, 27, 27, 27, 27, 27, 27, 27, 40, 40, 27, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 5, 19, 19, 1, 1, 33, 33, 33, 27, 27, 27, 27, 27, 6, 1, 1, 19, 19, 1, 1] 59 rigid atoms, others: [35, 36, 39, 40, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 178 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280466 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280466 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280466/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280466/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280466 Building REAL300000280467 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280467' /scratch/stefan/7769901/working/building/REAL300000280467 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280467 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280467/0 /scratch/stefan/7769901/working/building/REAL300000280467 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/664 `/scratch/stefan/7769901/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C(=O)[O-])=C2)C=C1) `REAL300000280467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280467 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 4, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 10, 10, 1, 1, 9, 13, 13, 13, 1, 1] 29 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280467 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 10, 9, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 13, 13, 29, 29, 13, 13, 5, 1, 1, 1, 13, 13] 29 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280467 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280467 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280467/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280467 Building REAL300000280468 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280468' /scratch/stefan/7769901/working/building/REAL300000280468 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280468 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280468/0 /scratch/stefan/7769901/working/building/REAL300000280468 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/665 `/scratch/stefan/7769901/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCC3)C=C1) `REAL300000280468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280468 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCC3)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 3, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 14, 14, 1, 1, 11, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280468 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC3=C2CCC3)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 70, 13, 13, 51, 51, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 107, 107, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 40, 39, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 419 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280468 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280468 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280468/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280468 Building REAL300000280469 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280469' /scratch/stefan/7769901/working/building/REAL300000280469 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280469 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280469/0 /scratch/stefan/7769901/working/building/REAL300000280469 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/666 `/scratch/stefan/7769901/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1) `REAL300000280469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280469 none CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 23, 39, 39, 23, 28, 83, 101, 101, 39, 39, 1, 1, 1, 1, 1, 1, 2, 2, 2, 39, 39, 101, 101, 39, 39, 1] 101 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 291 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280469 none CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 5, 24, 24, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 24, 24, 1, 1, 39] 101 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 164 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280469 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280469/1 /scratch/stefan/7769901/working/building/REAL300000280469 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/667 `/scratch/stefan/7769901/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1) `REAL300000280469.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280469 none CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 15, 33, 33, 15, 26, 87, 129, 129, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 33, 33, 129, 129, 33, 33, 1] 129 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 430 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280469 none CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 25, 25, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 25, 25, 1, 1, 33] 129 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 15, 16, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 162 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280469 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280469 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280469/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280469/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280469 Building REAL300000280470 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280470' /scratch/stefan/7769901/working/building/REAL300000280470 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280470 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280470/0 /scratch/stefan/7769901/working/building/REAL300000280470 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/668 `/scratch/stefan/7769901/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=C(OCCO3)C(C(=O)[O-])=C2)C=C1) `REAL300000280470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280470 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=C(OCCO3)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 55, 55, 39, 1, 1, 14, 14, 1, 1, 9, 39, 39, 39, 39, 39, 39, 1, 1] 112 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 25, 26, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280470 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=C(OCCO3)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 63, 26, 17, 39, 39, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 112, 112, 39, 39, 9, 1, 1, 1, 1, 1, 1, 39, 39] 112 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 466 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280470 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280470 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280470/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280470 Building REAL300000280471 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280471' /scratch/stefan/7769901/working/building/REAL300000280471 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280471 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280471/0 /scratch/stefan/7769901/working/building/REAL300000280471 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/669 `/scratch/stefan/7769901/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1) `REAL300000280471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280471 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 25, 25, 103, 140, 140, 49, 49, 1, 2, 2, 2, 1, 2, 49, 49, 140, 140, 49, 49, 1] 280 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 36, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 451 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280471 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 71, 71, 49, 49, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 7, 22, 22, 1, 1, 49, 49, 49, 49, 49, 98, 1, 1, 22, 22, 1, 1, 49] 280 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 345 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280471 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280471/1 /scratch/stefan/7769901/working/building/REAL300000280471 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/670 `/scratch/stefan/7769901/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1) `REAL300000280471.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280471 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 17, 59, 97, 97, 29, 29, 1, 2, 2, 2, 1, 2, 17, 29, 29, 97, 97, 29, 29, 1] 194 rigid atoms, others: [0, 1, 2, 3, 4, 37, 7, 8, 9, 10, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 362 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280471 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 38, 38, 29, 29, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 7, 21, 21, 1, 1, 29, 29, 29, 29, 29, 58, 6, 1, 1, 21, 21, 1, 1, 29] 194 rigid atoms, others: [32, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 219 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280471 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280471 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280471/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280471/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280471 Building REAL300000280472 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280472' /scratch/stefan/7769901/working/building/REAL300000280472 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280472 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280472/0 /scratch/stefan/7769901/working/building/REAL300000280472 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/671 `/scratch/stefan/7769901/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3OCC(C(=O)[O-])CC3=C2)C=C1) `REAL300000280472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280472 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3OCC(C(=O)[O-])CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 3, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 41, 41, 41, 41, 41, 41, 41, 68, 68, 41, 41, 41, 1, 1, 15, 15, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1] 146 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 266 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280472 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3OCC(C(=O)[O-])CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 73, 9, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 41, 41, 146, 146, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 146 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 564 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280472 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280472 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280472/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280472 Building REAL300000280473 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280473' /scratch/stefan/7769901/working/building/REAL300000280473 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280473 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280473/0 /scratch/stefan/7769901/working/building/REAL300000280473 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/672 `/scratch/stefan/7769901/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1) `REAL300000280473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280473 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 57, 57, 57, 85, 85, 57, 57, 57, 57, 57, 1, 1, 13, 13, 1, 1, 11, 57, 57, 1, 1] 151 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 310 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280473 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 79, 17, 17, 57, 57, 17, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 57, 57, 151, 151, 57, 57, 17, 1, 1, 57, 57] 151 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 592 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280473 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280473/1 /scratch/stefan/7769901/working/building/REAL300000280473 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/673 `/scratch/stefan/7769901/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1) `REAL300000280473.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280473 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 35, 35, 35, 47, 47, 35, 35, 35, 35, 35, 1, 1, 11, 11, 1, 1, 35, 35, 1, 1] 73 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30]) total number of confs: 183 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280473 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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, 45, 11, 11, 35, 35, 11, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 35, 35, 73, 73, 35, 35, 1, 1, 35, 35] 73 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 32, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 296 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280473 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280473 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280473/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280473/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280473 Building REAL300000280474 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280474' /scratch/stefan/7769901/working/building/REAL300000280474 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280474 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280474/0 /scratch/stefan/7769901/working/building/REAL300000280474 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/674 `/scratch/stefan/7769901/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1) `REAL300000280474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280474 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 86, 155, 155, 155, 21, 21, 21, 1, 1, 10, 10, 1, 1, 7, 21, 21, 155, 155, 21, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] 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]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280474 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 18, 13, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 31, 41, 41, 1, 1, 1, 21, 21, 79, 79, 21, 21, 9, 1, 1, 31, 31, 1, 21, 21] 201 rigid atoms, others: [32, 35, 9, 12, 13, 14, 15, 16, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280474 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280474 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280474/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280474 Building REAL300000280475 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280475' /scratch/stefan/7769901/working/building/REAL300000280475 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280475 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280475/0 /scratch/stefan/7769901/working/building/REAL300000280475 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/675 `/scratch/stefan/7769901/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000280475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280475 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 11, 11, 43, 74, 74, 13, 13, 1, 1, 1, 1, 7, 30, 45, 45, 2, 2, 2, 1, 9, 13, 13, 74, 74, 13, 13, 1, 1, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 18, 19, 20, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 395 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280475 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 6, 17, 17, 1, 1, 13, 13, 7, 13, 47, 127, 136, 136, 13, 13, 13, 13, 4, 1, 1, 17, 17, 1, 1, 13, 13, 127, 127] 201 rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40]) total number of confs: 533 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280475 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280475 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280475/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280475 Building REAL300000280476 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280476' /scratch/stefan/7769901/working/building/REAL300000280476 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280476 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280476/0 /scratch/stefan/7769901/working/building/REAL300000280476 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/676 `/scratch/stefan/7769901/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280476 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 25, 71, 97, 97, 31, 31, 2, 2, 2, 1, 1, 13, 31, 31, 97, 97, 31, 31] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 340 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280476 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 23, 23, 1, 1, 31, 31, 31, 31, 31, 6, 1, 1, 23, 23, 1, 1] 97 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 154 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280476 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280476/1 /scratch/stefan/7769901/working/building/REAL300000280476 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/677 `/scratch/stefan/7769901/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280476.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280476 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 37, 37, 19, 26, 76, 89, 89, 37, 37, 2, 2, 2, 1, 1, 37, 37, 89, 89, 37, 37] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 267 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280476 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 37, 37, 37, 37, 37, 1, 1, 22, 22, 1, 1] 89 rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 146 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280476 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280476 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280476/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280476/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280476 Building REAL300000280477 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280477' /scratch/stefan/7769901/working/building/REAL300000280477 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280477 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280477/0 /scratch/stefan/7769901/working/building/REAL300000280477 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/678 `/scratch/stefan/7769901/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(F)=C2)C=C1) `REAL300000280477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280477 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 4, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 96, 162, 174, 174, 21, 21, 21, 1, 1, 8, 8, 1, 1, 7, 21, 21, 162, 162, 21, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] 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]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280477 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 19, 13, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 41, 65, 65, 1, 1, 1, 21, 21, 72, 72, 21, 21, 9, 1, 1, 41, 41, 1, 21, 21] 201 rigid atoms, others: [32, 35, 9, 12, 13, 14, 15, 16, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280477 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280477 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280477/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280477 Building REAL300000280478 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280478' /scratch/stefan/7769901/working/building/REAL300000280478 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280478 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280478/0 /scratch/stefan/7769901/working/building/REAL300000280478 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/679 `/scratch/stefan/7769901/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280478 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 13, 48, 100, 100, 17, 17, 1, 1, 1, 3, 3, 26, 26, 26, 26, 26, 1, 1, 9, 17, 17, 100, 100, 17, 17, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 447 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280478 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 45, 17, 17, 17, 17, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 5, 22, 22, 1, 1, 17, 17, 17, 27, 27, 96, 96, 96, 96, 96, 17, 17, 4, 1, 1, 22, 22, 1, 1, 17] 201 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 427 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280478 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280478 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280478/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280478 Building REAL300000280479 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280479' /scratch/stefan/7769901/working/building/REAL300000280479 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280479 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280479/0 /scratch/stefan/7769901/working/building/REAL300000280479 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/680 `/scratch/stefan/7769901/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1) `REAL300000280479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280479 none CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 16, 48, 71, 71, 21, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 71, 71, 21, 21, 1] 71 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 249 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280479 none CC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 5, 20, 20, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 20, 20, 1, 1, 21] 71 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 15, 16, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 131 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280479 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280479/1 /scratch/stefan/7769901/working/building/REAL300000280479 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/681 `/scratch/stefan/7769901/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1) `REAL300000280479.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280479 none CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 11, 25, 25, 11, 15, 59, 79, 79, 25, 25, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 79, 79, 25, 25, 1] 79 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 250 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280479 none CC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 24, 24, 1, 1, 25] 79 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 146 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280479 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280479 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280479/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280479/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280479 Building REAL300000280480 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280480' /scratch/stefan/7769901/working/building/REAL300000280480 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280480 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280480/0 /scratch/stefan/7769901/working/building/REAL300000280480 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/682 `/scratch/stefan/7769901/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1) `REAL300000280480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280480 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 35, 35, 27, 31, 35, 35, 35, 35, 35, 1, 1, 12, 12, 1, 1, 11, 35, 35, 35, 1, 1] 73 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 187 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280480 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 15, 14, 35, 35, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 73, 73, 35, 35, 9, 1, 1, 1, 35, 35] 73 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 289 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280480 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280480/1 /scratch/stefan/7769901/working/building/REAL300000280480 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/683 `/scratch/stefan/7769901/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1) `REAL300000280480.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280480 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 35, 35, 31, 33, 35, 35, 35, 35, 35, 1, 1, 14, 14, 1, 1, 35, 35, 35, 1, 1] 62 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 172 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280480 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 41, 11, 11, 35, 35, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 62, 62, 35, 35, 1, 1, 1, 35, 35] 62 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 234 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280480 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280480 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280480/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280480/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280480 Building REAL300000280481 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280481' /scratch/stefan/7769901/working/building/REAL300000280481 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280481 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280481/0 /scratch/stefan/7769901/working/building/REAL300000280481 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/684 `/scratch/stefan/7769901/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1) `REAL300000280481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280481 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 41, 41, 41, 41, 65, 65, 41, 41, 41, 1, 1, 11, 11, 1, 1, 9, 41, 41, 41, 1, 1] 171 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 242 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280481 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [171, 171, 65, 9, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 41, 41, 171, 171, 41, 41, 9, 1, 1, 1, 41, 41] 171 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 682 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280481 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280481 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280481/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280481 Building REAL300000280482 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280482' /scratch/stefan/7769901/working/building/REAL300000280482 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280482 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280482/0 /scratch/stefan/7769901/working/building/REAL300000280482 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/685 `/scratch/stefan/7769901/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1) `REAL300000280482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280482 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 3, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 86, 86, 86, 86, 86, 86, 86, 1, 1, 16, 16, 1, 1, 86, 86, 1, 1] 144 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27]) total number of confs: 221 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280482 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 108, 24, 24, 86, 86, 24, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 144, 144, 86, 86, 1, 1, 86, 86] 144 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 540 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280482 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280482 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280482/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280482 Building REAL300000280483 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280483' /scratch/stefan/7769901/working/building/REAL300000280483 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280483 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280483/0 /scratch/stefan/7769901/working/building/REAL300000280483 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/686 `/scratch/stefan/7769901/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1) `REAL300000280483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280483 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 14, 14, 1, 1, 9, 28, 28, 28, 1, 1] 94 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 120 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280483 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 56, 26, 17, 28, 28, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 94, 94, 28, 28, 9, 1, 1, 1, 28, 28] 94 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 351 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280483 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280483/1 /scratch/stefan/7769901/working/building/REAL300000280483 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/687 `/scratch/stefan/7769901/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1) `REAL300000280483.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280483 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [16, 16, 4, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 16, 16, 1, 1, 33, 33, 33, 1, 1] 73 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 122 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280483 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 53, 21, 17, 33, 33, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 73, 73, 33, 33, 1, 1, 1, 33, 33] 73 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 262 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280483 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280483 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280483/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280483/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280483 Building REAL300000280484 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280484' /scratch/stefan/7769901/working/building/REAL300000280484 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280484 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280484/0 /scratch/stefan/7769901/working/building/REAL300000280484 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/688 `/scratch/stefan/7769901/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1F) `REAL300000280484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280484 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 68, 68, 25, 25, 136, 177, 177, 68, 68, 1, 1, 2, 2, 2, 1, 1, 68, 68, 177, 177, 68, 68] 177 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 540 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280484 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 68, 68, 68, 68, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 7, 29, 29, 1, 1, 68, 68, 68, 68, 68, 68, 68, 1, 1, 29, 29, 1, 1] 177 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 212 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280484 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280484/1 /scratch/stefan/7769901/working/building/REAL300000280484 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/689 `/scratch/stefan/7769901/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1F) `REAL300000280484.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280484 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 67, 67, 25, 25, 149, 201, 201, 67, 67, 1, 1, 2, 2, 2, 1, 1, 25, 67, 67, 201, 201, 67, 67] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 668 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280484 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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: [67, 67, 67, 67, 67, 67, 67, 67, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 27, 27, 1, 1, 67, 67, 67, 67, 67, 67, 67, 6, 1, 1, 27, 27, 1, 1] 201 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 205 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280484 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280484 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280484/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280484/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280484 Building REAL300000280485 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280485' /scratch/stefan/7769901/working/building/REAL300000280485 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280485 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280485/0 /scratch/stefan/7769901/working/building/REAL300000280485 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/690 `/scratch/stefan/7769901/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-]) `REAL300000280485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280485 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 9, 23, 23, 9, 14, 72, 129, 129, 23, 23, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 23, 23, 127, 128, 23, 23, 1] 180 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 431 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280485 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [48, 23, 23, 23, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 27, 27, 1, 1, 23, 23, 23, 23, 23, 41, 41, 48, 48, 48, 23, 1, 1, 27, 27, 1, 1, 23] 180 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 262 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280485 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280485/1 /scratch/stefan/7769901/working/building/REAL300000280485 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/691 `/scratch/stefan/7769901/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-]) `REAL300000280485.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280485 none COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 5, 5, 5, 8, 20, 20, 8, 16, 66, 142, 142, 20, 20, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 8, 20, 20, 142, 142, 20, 20, 1] 188 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 503 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280485 none COC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 20, 20, 20, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 27, 27, 1, 1, 20, 20, 20, 20, 20, 33, 33, 39, 39, 39, 20, 6, 1, 1, 27, 27, 1, 1, 20] 188 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 236 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280485 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280485 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280485/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280485/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280485 Building REAL300000280486 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280486' /scratch/stefan/7769901/working/building/REAL300000280486 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280486 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280486/0 /scratch/stefan/7769901/working/building/REAL300000280486 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/692 `/scratch/stefan/7769901/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1) `REAL300000280486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280486 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 71, 71, 53, 71, 71, 71, 71, 71, 71, 1, 1, 14, 14, 1, 1, 71, 71, 71, 1, 1] 119 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 264 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280486 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 91, 25, 25, 71, 71, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 71, 71, 119, 119, 71, 71, 1, 1, 1, 71, 71] 119 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 440 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280486 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280486/1 /scratch/stefan/7769901/working/building/REAL300000280486 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/693 `/scratch/stefan/7769901/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1) `REAL300000280486.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280486 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 76, 76, 50, 76, 76, 76, 76, 76, 76, 1, 1, 14, 14, 1, 1, 11, 76, 76, 76, 1, 1] 141 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 308 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280486 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 97, 25, 25, 76, 76, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 76, 76, 141, 141, 76, 76, 25, 1, 1, 1, 76, 76] 141 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 574 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280486 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280486 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280486/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280486/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280486 Building REAL300000280487 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280487' /scratch/stefan/7769901/working/building/REAL300000280487 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280487 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280487/0 /scratch/stefan/7769901/working/building/REAL300000280487 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/694 `/scratch/stefan/7769901/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1) `REAL300000280487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280487 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 31, 31, 31, 31, 45, 45, 31, 31, 31, 1, 1, 11, 11, 1, 1, 9, 31, 31, 31, 1, 1] 119 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 172 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280487 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 55, 9, 9, 31, 31, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 31, 31, 119, 119, 31, 31, 9, 1, 1, 1, 31, 31] 119 rigid atoms, others: [9, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 472 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280487 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280487 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280487/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280487 Building REAL300000280488 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280488' /scratch/stefan/7769901/working/building/REAL300000280488 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280488 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280488/0 /scratch/stefan/7769901/working/building/REAL300000280488 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/695 `/scratch/stefan/7769901/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280488 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 25, 72, 97, 97, 31, 31, 2, 2, 2, 1, 1, 13, 31, 31, 97, 97, 31, 31] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 335 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280488 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 23, 23, 1, 1, 31, 31, 31, 31, 31, 6, 1, 1, 23, 23, 1, 1] 97 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 154 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280488 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280488 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280488/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280488 Building REAL300000280489 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280489' /scratch/stefan/7769901/working/building/REAL300000280489 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280489 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280489/0 /scratch/stefan/7769901/working/building/REAL300000280489 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/696 `/scratch/stefan/7769901/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1) `REAL300000280489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280489 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 3, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 30, 30, 40, 44, 48, 48, 11, 11, 1, 1, 9, 9, 1, 1, 5, 11, 11, 40, 40, 44, 44, 11, 11, 1, 1] 72 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280489 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 17, 5, 5, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 15, 17, 25, 25, 1, 1, 11, 11, 29, 29, 11, 11, 5, 1, 1, 15, 15, 17, 17, 1, 1, 11, 11] 72 rigid atoms, others: [32, 33, 38, 39, 9, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41]) total number of confs: 202 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280489 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280489/1 /scratch/stefan/7769901/working/building/REAL300000280489 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/697 `/scratch/stefan/7769901/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1) `REAL300000280489.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280489 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 73, 73, 139, 139, 162, 148, 13, 13, 1, 1, 5, 6, 1, 1, 13, 13, 139, 139, 139, 139, 13, 13, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280489 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)CCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 5, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 43, 43, 64, 54, 1, 1, 13, 13, 34, 34, 13, 13, 1, 1, 43, 43, 43, 43, 1, 1, 13, 13] 201 rigid atoms, others: [32, 37, 38, 9, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280489 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280489 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280489/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280489/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280489 Building REAL300000280490 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280490' /scratch/stefan/7769901/working/building/REAL300000280490 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280490 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280490/0 /scratch/stefan/7769901/working/building/REAL300000280490 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/698 `/scratch/stefan/7769901/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280490 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 63, 63, 41, 1, 1, 16, 16, 1, 1, 9, 41, 41, 1, 1] 145 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 249 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280490 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 73, 24, 17, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 145, 145, 41, 41, 9, 1, 1, 41, 41] 145 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 564 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280490 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280490/1 /scratch/stefan/7769901/working/building/REAL300000280490 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/699 `/scratch/stefan/7769901/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280490.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280490 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 71, 71, 47, 1, 1, 14, 14, 1, 1, 47, 47, 1, 1] 132 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30]) total number of confs: 254 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280490 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 87, 24, 17, 47, 47, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 132, 132, 47, 47, 1, 1, 47, 47] 132 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 32, 20, 21, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 470 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280490 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280490 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280490/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280490/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280490 Building REAL300000280491 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280491' /scratch/stefan/7769901/working/building/REAL300000280491 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280491 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280491/0 /scratch/stefan/7769901/working/building/REAL300000280491 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/700 `/scratch/stefan/7769901/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280491 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 4, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 17, 17, 1, 1, 9, 32, 32, 32, 1, 1] 85 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) total number of confs: 141 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280491 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 27, 17, 32, 32, 9, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 32, 32, 85, 85, 32, 32, 9, 1, 1, 1, 32, 32] 85 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 345 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280491 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280491/1 /scratch/stefan/7769901/working/building/REAL300000280491 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/701 `/scratch/stefan/7769901/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280491.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280491 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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, 4, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 16, 16, 1, 1, 31, 31, 31, 1, 1] 65 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 129 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280491 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 47, 20, 17, 31, 31, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 65, 65, 31, 31, 1, 1, 1, 31, 31] 65 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 34, 33, 24, 25, 26, 27, 28, 29]) total number of confs: 231 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280491 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280491 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280491/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280491/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280491 Building REAL300000280492 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280492' /scratch/stefan/7769901/working/building/REAL300000280492 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280492 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280492/0 /scratch/stefan/7769901/working/building/REAL300000280492 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/702 `/scratch/stefan/7769901/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1) `REAL300000280492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280492 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 266 conformations in input total number of sets (complete confs): 266 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 3, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 13, 13, 1, 1, 83, 83, 83, 166, 1, 1] 266 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 368 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280492 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 266 conformations in input total number of sets (complete confs): 266 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 105, 25, 25, 83, 83, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 133, 133, 83, 83, 1, 1, 1, 2, 83, 83] 266 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 33, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 484 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280492 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280492/1 /scratch/stefan/7769901/working/building/REAL300000280492 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/703 `/scratch/stefan/7769901/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1) `REAL300000280492.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280492 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 16, 16, 1, 1, 11, 29, 29, 29, 1, 1] 55 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 139 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280492 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 35, 9, 7, 29, 29, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 29, 29, 55, 55, 29, 29, 7, 1, 1, 1, 29, 29] 55 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 225 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280492 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280492 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280492/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280492/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280492 Building REAL300000280493 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280493' /scratch/stefan/7769901/working/building/REAL300000280493 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280493 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280493/0 /scratch/stefan/7769901/working/building/REAL300000280493 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/704 `/scratch/stefan/7769901/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000280493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280493 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 21, 25, 25, 13, 13, 1, 1, 13, 13, 1, 1, 7, 13, 13, 21, 21, 13, 13, 1, 1] 61 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 22, 23, 36, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280493 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 23, 7, 5, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 13, 13, 47, 47, 13, 13, 5, 1, 1, 2, 2, 1, 1, 13, 13] 61 rigid atoms, others: [33, 34, 9, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36]) total number of confs: 199 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280493 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280493 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280493/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280493 Building REAL300000280494 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280494' /scratch/stefan/7769901/working/building/REAL300000280494 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280494 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280494/0 /scratch/stefan/7769901/working/building/REAL300000280494 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/705 `/scratch/stefan/7769901/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280494 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 4, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 43, 43, 43, 43, 43, 43, 43, 66, 66, 43, 1, 1, 16, 16, 1, 1, 9, 43, 43, 1, 1] 151 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 257 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280494 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC(Cl)=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 77, 28, 17, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 151, 151, 43, 43, 9, 1, 1, 43, 43] 151 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 590 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280494 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280494 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280494/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280494 Building REAL300000280495 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280495' /scratch/stefan/7769901/working/building/REAL300000280495 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280495 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280495/0 /scratch/stefan/7769901/working/building/REAL300000280495 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/706 `/scratch/stefan/7769901/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000280495 0 /scratch/stefan/7769901/working/building/REAL300000280495 /scratch/stefan/7769901/working /scratch/stefan/7769901 `0' -> `0.failed' Finished preparing REAL300000280495 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Found failed protomers Marking REAL300000280495 as failed `/scratch/stefan/7769901/working/building/REAL300000280495' -> `/scratch/stefan/7769901/failed/REAL300000280495' Building REAL300000280496 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280496' /scratch/stefan/7769901/working/building/REAL300000280496 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280496 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280496/0 /scratch/stefan/7769901/working/building/REAL300000280496 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/707 `/scratch/stefan/7769901/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1F) `REAL300000280496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280496 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 17, 18, 73, 145, 145, 25, 25, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 25, 25, 145, 145, 25, 25, 1] 145 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 23, 24, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 507 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280496 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 27, 27, 1, 1, 25, 25, 25, 37, 37, 25, 25, 25, 25, 25, 25, 6, 1, 1, 27, 27, 1, 1, 25] 145 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 196 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280496 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280496 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280496/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280496 Building REAL300000280497 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280497' /scratch/stefan/7769901/working/building/REAL300000280497 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280497 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280497/0 /scratch/stefan/7769901/working/building/REAL300000280497 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/708 `/scratch/stefan/7769901/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280497 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 24, 24, 11, 11, 47, 72, 72, 24, 24, 2, 2, 2, 1, 1, 1, 11, 24, 24, 72, 72, 24, 24] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 263 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280497 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 18, 18, 24, 24, 24, 24, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 6, 19, 19, 1, 1, 24, 24, 24, 24, 24, 24, 6, 1, 1, 19, 19, 1, 1] 72 rigid atoms, others: [32, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 168 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280497 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280497 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280497/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280497 Building REAL300000280498 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280498' /scratch/stefan/7769901/working/building/REAL300000280498 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280498 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280498/0 /scratch/stefan/7769901/working/building/REAL300000280498 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/709 `/scratch/stefan/7769901/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1C) `REAL300000280498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280498 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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, 3, 3, 3, 9, 15, 15, 13, 14, 43, 75, 75, 15, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 9, 15, 15, 75, 75, 15, 15, 1, 2, 2, 2] 75 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 23, 24, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280498 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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: [15, 15, 15, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 6, 19, 19, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 19, 19, 1, 1, 15, 15, 15, 15] 75 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280498 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280498 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280498/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280498 Building REAL300000280499 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280499' /scratch/stefan/7769901/working/building/REAL300000280499 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280499 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280499/0 /scratch/stefan/7769901/working/building/REAL300000280499 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/710 `/scratch/stefan/7769901/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1) `REAL300000280499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280499 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 9, 9, 1, 1, 9, 27, 27, 27, 1, 1] 67 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280499 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 45, 9, 9, 27, 27, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 27, 27, 67, 67, 27, 27, 9, 1, 1, 1, 27, 27] 67 rigid atoms, others: [32, 33, 9, 12, 13, 14, 15, 16, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280499 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280499/1 /scratch/stefan/7769901/working/building/REAL300000280499 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/711 `/scratch/stefan/7769901/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1) `REAL300000280499.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280499 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 11, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 11, 11, 1, 1, 32, 32, 32, 1, 1] 64 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280499 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 45, 9, 9, 32, 32, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 32, 32, 64, 64, 32, 32, 1, 1, 1, 32, 32] 64 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 249 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280499 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280499 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280499/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280499/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280499 Building REAL300000280500 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280500' /scratch/stefan/7769901/working/building/REAL300000280500 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280500 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280500/0 /scratch/stefan/7769901/working/building/REAL300000280500 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/712 `/scratch/stefan/7769901/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2F)C=C1) `REAL300000280500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280500 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 14, 14, 1, 1, 97, 97, 1, 1] 169 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 23, 24, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30]) total number of confs: 233 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280500 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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, 119, 25, 25, 97, 97, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 97, 97, 169, 169, 97, 97, 1, 1, 97, 97] 169 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 32, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 636 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280500 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280500 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280500/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280500 Building REAL300000280501 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280501' /scratch/stefan/7769901/working/building/REAL300000280501 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280501 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280501/0 /scratch/stefan/7769901/working/building/REAL300000280501 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/713 `/scratch/stefan/7769901/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1C(=O)[O-]) `REAL300000280501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280501 none CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 16, 43, 61, 61, 19, 19, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 11, 19, 19, 61, 61, 19, 19, 2, 2, 2] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 228 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280501 none CC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 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: [19, 19, 19, 19, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 5, 19, 19, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 19, 19, 1, 1, 19, 19, 19] 61 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280501 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280501 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280501/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280501 Building REAL300000280502 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280502' /scratch/stefan/7769901/working/building/REAL300000280502 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280502 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280502/0 /scratch/stefan/7769901/working/building/REAL300000280502 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/714 `/scratch/stefan/7769901/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280502 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 58, 58, 25, 25, 135, 201, 201, 58, 58, 1, 1, 1, 3, 3, 2, 2, 2, 1, 58, 58, 201, 201, 58, 58, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 690 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280502 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 24, 24, 1, 1, 58, 58, 58, 95, 95, 58, 58, 58, 58, 1, 1, 24, 24, 1, 1, 58] 201 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 324 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280502 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280502/1 /scratch/stefan/7769901/working/building/REAL300000280502 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/715 `/scratch/stefan/7769901/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280502.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000280502 1 /scratch/stefan/7769901/working/building/REAL300000280502 /scratch/stefan/7769901/working /scratch/stefan/7769901 `1' -> `1.failed' Finished preparing REAL300000280502 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Found failed protomers Marking REAL300000280502 as failed `/scratch/stefan/7769901/working/building/REAL300000280502' -> `/scratch/stefan/7769901/failed/REAL300000280502' Building REAL300000280503 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280503' /scratch/stefan/7769901/working/building/REAL300000280503 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280503 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280503/0 /scratch/stefan/7769901/working/building/REAL300000280503 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/716 `/scratch/stefan/7769901/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1Cl) `REAL300000280503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280503 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 13, 50, 72, 72, 31, 31, 1, 1, 2, 2, 2, 1, 1, 31, 31, 72, 72, 31, 31] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 249 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280503 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 31, 31, 31, 31, 31, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 31, 31, 31, 31, 31, 31, 31, 1, 1, 23, 23, 1, 1] 72 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 149 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280503 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280503/1 /scratch/stefan/7769901/working/building/REAL300000280503 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/717 `/scratch/stefan/7769901/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1Cl) `REAL300000280503.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280503 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 35, 35, 17, 17, 61, 89, 89, 35, 35, 1, 1, 2, 2, 2, 1, 1, 17, 35, 35, 89, 89, 35, 35] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 320 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280503 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 21, 21, 1, 1, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 21, 21, 1, 1] 89 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 150 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280503 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280503 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280503/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280503/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280503 Building REAL300000280504 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280504' /scratch/stefan/7769901/working/building/REAL300000280504 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280504 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280504/0 /scratch/stefan/7769901/working/building/REAL300000280504 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/718 `/scratch/stefan/7769901/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1) `REAL300000280504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280504 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 25, 60, 60, 25, 25, 141, 201, 201, 60, 60, 1, 2, 2, 2, 1, 60, 60, 201, 201, 60, 60, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 35, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 661 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280504 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 95, 95, 60, 60, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 22, 22, 1, 1, 60, 60, 60, 60, 60, 1, 1, 22, 22, 1, 1, 60] 201 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 315 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280504 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280504/1 /scratch/stefan/7769901/working/building/REAL300000280504 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/719 `/scratch/stefan/7769901/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1) `REAL300000280504.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280504 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 29, 32, 128, 201, 201, 47, 47, 1, 2, 2, 2, 1, 23, 47, 47, 201, 201, 47, 47, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 36, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 662 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280504 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [47, 47, 47, 47, 47, 80, 80, 47, 47, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 25, 25, 1, 1, 47, 47, 47, 47, 47, 6, 1, 1, 25, 25, 1, 1, 47] 201 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 306 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280504 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280504 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280504/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280504/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280504 Building REAL300000280505 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280505' /scratch/stefan/7769901/working/building/REAL300000280505 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280505 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280505/0 /scratch/stefan/7769901/working/building/REAL300000280505 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/720 `/scratch/stefan/7769901/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280505 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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: [6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 9, 13, 49, 85, 85, 15, 15, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 9, 15, 15, 85, 85, 15, 15, 1] 167 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 319 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280505 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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: [39, 15, 15, 15, 15, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 15, 15, 15, 19, 19, 39, 39, 39, 39, 39, 15, 15, 6, 1, 1, 24, 24, 1, 1, 15] 167 rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) total number of confs: 239 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280505 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280505 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280505/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280505 Building REAL300000280506 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280506' /scratch/stefan/7769901/working/building/REAL300000280506 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280506 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280506/0 /scratch/stefan/7769901/working/building/REAL300000280506 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/721 `/scratch/stefan/7769901/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1CC(=O)[O-]) `REAL300000280506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280506 none COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 7, 9, 19, 31, 31, 11, 11, 1, 1, 1, 3, 7, 7, 3, 3, 3, 1, 1, 7, 11, 11, 31, 31, 11, 11, 1, 3, 3] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280506 none COC1=CC=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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] 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: [17, 11, 11, 11, 11, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 16, 16, 1, 1, 11, 11, 11, 11, 13, 13, 17, 17, 17, 11, 11, 4, 1, 1, 16, 16, 1, 1, 11, 11, 11] 31 rigid atoms, others: [32, 33, 36, 37, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280506 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280506 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280506/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280506 Building REAL300000280507 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280507' /scratch/stefan/7769901/working/building/REAL300000280507 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280507 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280507/0 /scratch/stefan/7769901/working/building/REAL300000280507 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/722 `/scratch/stefan/7769901/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280507 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 21, 21, 11, 18, 45, 65, 65, 21, 21, 2, 2, 2, 1, 1, 11, 21, 21, 65, 65, 21, 21] 65 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 28, 29] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 248 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280507 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 5, 17, 17, 1, 1, 21, 21, 21, 21, 21, 6, 1, 1, 17, 17, 1, 1] 65 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 116 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280507 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280507/1 /scratch/stefan/7769901/working/building/REAL300000280507 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/723 `/scratch/stefan/7769901/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280507.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280507 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 17, 51, 68, 68, 29, 29, 2, 2, 2, 1, 1, 29, 29, 68, 68, 29, 29] 68 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 28, 29] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280507 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 6, 18, 18, 1, 1, 29, 29, 29, 29, 29, 1, 1, 18, 18, 1, 1] 68 rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 123 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280507 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280507 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280507/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280507/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280507 Building REAL300000280508 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280508' /scratch/stefan/7769901/working/building/REAL300000280508 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280508 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280508/0 /scratch/stefan/7769901/working/building/REAL300000280508 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/724 `/scratch/stefan/7769901/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1Cl) `REAL300000280508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280508 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 12, 13, 54, 90, 90, 15, 15, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 15, 15, 90, 90, 15, 15, 1] 90 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 23, 24, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280508 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 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: [15, 15, 15, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 7, 20, 20, 1, 1, 15, 15, 15, 23, 23, 15, 15, 15, 15, 15, 15, 6, 1, 1, 20, 20, 1, 1, 15] 90 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 127 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280508 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280508 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280508/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280508 Building REAL300000280509 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280509' /scratch/stefan/7769901/working/building/REAL300000280509 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280509 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280509/0 /scratch/stefan/7769901/working/building/REAL300000280509 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/725 `/scratch/stefan/7769901/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280509 none CCN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 9, 18, 66, 126, 126, 25, 25, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 9, 25, 25, 126, 126, 25, 25, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 477 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280509 none CCN1C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 25, 25, 25, 25, 25, 54, 54, 54, 54, 54, 25, 6, 1, 1, 22, 22, 1, 1, 25] 201 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 270 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280509 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280509/1 /scratch/stefan/7769901/working/building/REAL300000280509 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/726 `/scratch/stefan/7769901/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280509.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280509 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 9, 16, 75, 128, 128, 28, 28, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 28, 28, 128, 128, 28, 28, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 461 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280509 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 28, 28, 28, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 28, 28, 28, 28, 28, 70, 70, 70, 70, 70, 28, 1, 1, 24, 24, 1, 1, 28] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 349 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280509 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280509 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280509/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280509/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280509 Building REAL300000280510 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280510' /scratch/stefan/7769901/working/building/REAL300000280510 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280510 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280510/0 /scratch/stefan/7769901/working/building/REAL300000280510 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/727 `/scratch/stefan/7769901/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1CC(=O)[O-]) `REAL300000280510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280510 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 1, 5, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 9, 28, 42, 42, 13, 13, 1, 1, 1, 1, 3, 7, 7, 2, 2, 2, 1, 2, 2, 2, 5, 13, 13, 42, 42, 13, 13, 2, 2, 2, 3, 3] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 194 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280510 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 5, 1, 5, 1, 11, 11, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 5, 19, 19, 1, 1, 13, 13, 13, 13, 16, 25, 25, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 19, 19, 1, 1, 13, 13, 13, 16, 16] 49 rigid atoms, others: [35, 36, 39, 40, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280510 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280510 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280510/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280510 Building REAL300000280511 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280511' /scratch/stefan/7769901/working/building/REAL300000280511 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280511 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280511/0 /scratch/stefan/7769901/working/building/REAL300000280511 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/728 `/scratch/stefan/7769901/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280511 none CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 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, 3, 3, 3, 9, 21, 21, 16, 19, 65, 127, 127, 21, 21, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 21, 21, 127, 127, 21, 21, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 463 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280511 none CC1=C(Cl)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 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, 21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 25, 25, 1, 1, 21, 21, 21, 32, 32, 21, 21, 21, 21, 6, 1, 1, 25, 25, 1, 1, 21] 127 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 176 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280511 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280511 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280511/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280511 Building REAL300000280512 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280512' /scratch/stefan/7769901/working/building/REAL300000280512 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280512 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280512/0 /scratch/stefan/7769901/working/building/REAL300000280512 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/729 `/scratch/stefan/7769901/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1) `REAL300000280512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280512 none CC(C)(C)C1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 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, 6, 6, 4, 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] 0 hydrogens 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, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 2, 4, 12, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 17, 17, 5, 5, 1] 17 rigid atoms, others: [1, 4, 5, 6, 42, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280512 none CC(C)(C)C1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 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, 6, 6, 4, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 14, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 14, 14, 1, 1, 5] 17 rigid atoms, others: [36, 37, 40, 9, 10, 11, 12, 13, 14, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42]) total number of confs: 55 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280512 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280512/1 /scratch/stefan/7769901/working/building/REAL300000280512 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/730 `/scratch/stefan/7769901/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1) `REAL300000280512.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280512 none CC(C)(C)C1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 7, 12, 12, 7, 9, 27, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 29, 29, 12, 12, 1] 29 rigid atoms, others: [1, 4, 5, 6, 41, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280512 none CC(C)(C)C1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [12, 12, 12, 12, 12, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 5, 14, 14, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 15, 15, 1, 1, 12] 29 rigid atoms, others: [35, 36, 39, 40, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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 /scratch/stefan/7769901/working/building/REAL300000280512 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280512 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280512/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280512/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280512 Building REAL300000280513 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280513' /scratch/stefan/7769901/working/building/REAL300000280513 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280513 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280513/0 /scratch/stefan/7769901/working/building/REAL300000280513 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/731 `/scratch/stefan/7769901/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280513 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 25, 25, 11, 20, 78, 134, 134, 25, 25, 1, 1, 1, 3, 3, 4, 4, 4, 1, 11, 25, 25, 134, 134, 25, 25, 1] 196 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 494 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280513 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 25, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 25, 25, 1, 1, 25, 25, 25, 45, 45, 51, 51, 51, 25, 6, 1, 1, 25, 25, 1, 1, 25] 196 rigid atoms, others: [32, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 276 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280513 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280513/1 /scratch/stefan/7769901/working/building/REAL300000280513 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/732 `/scratch/stefan/7769901/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280513.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280513 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 29, 29, 13, 19, 76, 143, 143, 29, 29, 1, 1, 1, 3, 3, 4, 4, 4, 1, 29, 29, 143, 142, 29, 29, 1] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 530 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280513 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [55, 29, 29, 29, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 29, 29, 29, 47, 47, 55, 55, 55, 29, 1, 1, 24, 24, 1, 1, 29] 179 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 269 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280513 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280513 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280513/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280513/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280513 Building REAL300000280514 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280514' /scratch/stefan/7769901/working/building/REAL300000280514 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280514 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280514/0 /scratch/stefan/7769901/working/building/REAL300000280514 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/733 `/scratch/stefan/7769901/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1C(=O)[O-]) `REAL300000280514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280514 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 21, 21, 15, 15, 71, 163, 163, 21, 21, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 21, 21, 163, 163, 21, 21, 1, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 576 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280514 none CC1=CC(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 7, 22, 22, 1, 1, 21, 21, 21, 21, 35, 35, 21, 21, 21, 21, 4, 1, 1, 22, 22, 1, 1, 21, 21] 163 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36]) total number of confs: 179 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280514 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280514 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280514/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280514 Building REAL300000280515 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280515' /scratch/stefan/7769901/working/building/REAL300000280515 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280515 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280515/0 /scratch/stefan/7769901/working/building/REAL300000280515 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/734 `/scratch/stefan/7769901/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2[N+](=O)[O-])C=C1) `REAL300000280515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280515 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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: [12, 12, 4, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 22, 22, 22, 37, 42, 42, 22, 22, 22, 22, 22, 1, 1, 12, 12, 1, 1, 22, 22, 37, 37, 22, 1, 1] 74 rigid atoms, others: [3, 4, 5, 6, 7, 8, 37, 25, 26, 29, 30, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280515 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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: [49, 49, 26, 5, 5, 22, 22, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 22, 22, 49, 49, 22, 22, 1, 1, 2, 2, 1, 22, 22] 74 rigid atoms, others: [32, 35, 9, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37]) total number of confs: 212 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280515 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280515 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280515/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280515 Building REAL300000280516 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280516' /scratch/stefan/7769901/working/building/REAL300000280516 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280516 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280516/0 /scratch/stefan/7769901/working/building/REAL300000280516 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/735 `/scratch/stefan/7769901/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280516 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 5, 13, 34, 34, 15, 17, 99, 172, 172, 34, 34, 2, 2, 2, 1, 1, 13, 34, 34, 172, 172, 34, 34] 172 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 607 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280516 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 60, 60, 34, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 25, 25, 1, 1, 34, 34, 34, 34, 34, 6, 1, 1, 25, 25, 1, 1] 172 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 268 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280516 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280516 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280516/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280516 Building REAL300000280517 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280517' /scratch/stefan/7769901/working/building/REAL300000280517 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280517 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280517/0 /scratch/stefan/7769901/working/building/REAL300000280517 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/736 `/scratch/stefan/7769901/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2[N+](=O)[O-])C=C1) `REAL300000280517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280517 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 3, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 10, 10, 1, 1, 21, 21, 21, 1, 1] 41 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280517 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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, 5, 5, 21, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 21, 41, 41, 21, 21, 1, 1, 1, 21, 21] 41 rigid atoms, others: [32, 9, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 163 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280517 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280517 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280517/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280517 Building REAL300000280518 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280518' /scratch/stefan/7769901/working/building/REAL300000280518 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280518 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280518/0 /scratch/stefan/7769901/working/building/REAL300000280518 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/737 `/scratch/stefan/7769901/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1) `REAL300000280518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280518 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 85, 85, 85, 85, 85, 113, 113, 85, 85, 1, 1, 13, 13, 1, 1, 85, 85, 85, 1, 1] 151 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30]) total number of confs: 311 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280518 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 108, 25, 25, 85, 85, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 85, 85, 151, 151, 85, 85, 1, 1, 1, 85, 85] 151 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 585 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280518 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280518/1 /scratch/stefan/7769901/working/building/REAL300000280518 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/738 `/scratch/stefan/7769901/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1) `REAL300000280518.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280518 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 81, 81, 81, 81, 81, 124, 124, 81, 81, 1, 1, 13, 13, 1, 1, 11, 81, 81, 81, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31]) total number of confs: 380 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280518 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 24, 24, 81, 81, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 81, 81, 201, 201, 81, 81, 24, 1, 1, 1, 81, 81] 201 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 759 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280518 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280518 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280518/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280518/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280518 Building REAL300000280519 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280519' /scratch/stefan/7769901/working/building/REAL300000280519 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280519 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280519/0 /scratch/stefan/7769901/working/building/REAL300000280519 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/739 `/scratch/stefan/7769901/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280519 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 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, 1, 1, 3, 3, 3, 9, 21, 21, 16, 17, 63, 123, 123, 21, 21, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 21, 21, 123, 123, 21, 21, 1] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 445 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280519 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 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: [21, 21, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 25, 25, 1, 1, 21, 21, 21, 32, 32, 21, 21, 21, 21, 6, 1, 1, 25, 25, 1, 1, 21] 123 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 176 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280519 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280519/1 /scratch/stefan/7769901/working/building/REAL300000280519 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/740 `/scratch/stefan/7769901/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-]) `REAL300000280519.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280519 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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, 2, 2, 2, 9, 25, 25, 15, 15, 68, 100, 100, 25, 25, 1, 1, 1, 3, 3, 2, 2, 2, 1, 25, 25, 100, 100, 25, 25, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 330 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280519 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 25, 25, 25, 38, 38, 25, 25, 25, 25, 1, 1, 23, 23, 1, 1, 25] 100 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 182 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280519 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280519 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280519/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280519/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280519 Building REAL300000280520 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280520' /scratch/stefan/7769901/working/building/REAL300000280520 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280520 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280520/0 /scratch/stefan/7769901/working/building/REAL300000280520 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/741 `/scratch/stefan/7769901/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1) `REAL300000280520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280520 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 41, 41, 29, 1, 1, 11, 11, 1, 1, 9, 29, 29, 29, 29, 29, 29, 1, 1] 85 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 25, 26, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280520 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 9, 9, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 85, 85, 29, 29, 9, 1, 1, 1, 1, 1, 1, 29, 29] 85 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 334 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280520 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280520/1 /scratch/stefan/7769901/working/building/REAL300000280520 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/742 `/scratch/stefan/7769901/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1) `REAL300000280520.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280520 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 4, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 48, 48, 32, 1, 1, 12, 12, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1] 78 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 38, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280520 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 58, 18, 17, 32, 32, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 78, 78, 32, 32, 1, 1, 1, 1, 1, 1, 32, 32] 78 rigid atoms, others: [32, 33, 34, 35, 36, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 268 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280520 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280520 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280520/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280520/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280520 Building REAL300000280521 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280521' /scratch/stefan/7769901/working/building/REAL300000280521 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280521 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280521/0 /scratch/stefan/7769901/working/building/REAL300000280521 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/743 `/scratch/stefan/7769901/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1) `REAL300000280521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280521 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 14, 14, 1, 1, 115, 115, 115, 1, 1] 187 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29]) total number of confs: 268 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280521 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 157, 72, 49, 115, 115, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 115, 115, 187, 187, 115, 115, 1, 1, 1, 115, 115] 187 rigid atoms, others: [9, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 663 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280521 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280521 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280521/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280521 Building REAL300000280522 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280522' /scratch/stefan/7769901/working/building/REAL300000280522 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280522 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280522/0 /scratch/stefan/7769901/working/building/REAL300000280522 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/744 `/scratch/stefan/7769901/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1) `REAL300000280522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280522 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 23, 48, 48, 23, 33, 108, 146, 146, 48, 48, 3, 3, 3, 1, 1, 1, 48, 48, 146, 146, 48, 48] 146 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 28, 29, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 494 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280522 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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: [68, 48, 48, 48, 31, 48, 48, 48, 48, 48, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 68, 68, 68, 48, 48, 48, 1, 1, 22, 22, 1, 1] 146 rigid atoms, others: [32, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 265 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280522 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280522/1 /scratch/stefan/7769901/working/building/REAL300000280522 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/745 `/scratch/stefan/7769901/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1) `REAL300000280522.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280522 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 23, 33, 33, 23, 30, 81, 121, 121, 33, 33, 4, 4, 4, 1, 1, 1, 23, 33, 33, 121, 121, 33, 33] 121 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 28, 29, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 420 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280522 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(OCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 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: [35, 33, 33, 33, 27, 33, 33, 33, 33, 33, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 5, 21, 21, 1, 1, 35, 35, 35, 33, 33, 33, 6, 1, 1, 21, 21, 1, 1] 121 rigid atoms, others: [32, 33, 36, 37, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 180 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280522 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280522 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280522/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280522/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280522 Building REAL300000280523 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280523' /scratch/stefan/7769901/working/building/REAL300000280523 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280523 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280523/0 /scratch/stefan/7769901/working/building/REAL300000280523 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/746 `/scratch/stefan/7769901/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1) `REAL300000280523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280523 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 13, 13, 1, 1, 75, 1, 1] 139 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27]) total number of confs: 198 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280523 none N#CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 87, 23, 23, 75, 75, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 139, 139, 75, 75, 1, 75, 75] 139 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 570 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280523 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280523 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280523/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280523 Building REAL300000280524 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280524' /scratch/stefan/7769901/working/building/REAL300000280524 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280524 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280524/0 /scratch/stefan/7769901/working/building/REAL300000280524 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/747 `/scratch/stefan/7769901/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1) `REAL300000280524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280524 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 86, 37, 37, 53, 53, 20, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 1, 1, 7, 7, 53, 53, 115, 115, 53, 53, 20, 7, 7, 1, 1, 1, 1, 7, 7, 53, 53] 115 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 400 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280524 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 3, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 53, 69, 69, 53, 53, 15, 15, 1, 1, 10, 10, 1, 1, 7, 15, 15, 53, 53, 53, 53, 15, 15, 1, 1] 115 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 245 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280524 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C3(C(=O)[O-])CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 68, 28, 9, 9, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 10, 10, 7, 7, 1, 1, 15, 15, 66, 66, 15, 15, 5, 1, 1, 7, 7, 7, 7, 1, 1, 15, 15] 115 rigid atoms, others: [32, 37, 38, 9, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 291 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280524 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280524 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280524/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280524 Building REAL300000280525 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280525' /scratch/stefan/7769901/working/building/REAL300000280525 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280525 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280525/0 /scratch/stefan/7769901/working/building/REAL300000280525 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/748 `/scratch/stefan/7769901/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=C2)C=C1) `REAL300000280525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280525 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 4, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 18, 18, 18, 18, 18, 18, 24, 24, 18, 18, 18, 1, 1, 10, 10, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280525 none N#CCOC1=CC=C(NS(=O)(=O)C2=CC=C3CC(C(=O)[O-])CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 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, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 32, 16, 13, 18, 18, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 18, 18, 42, 42, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 42 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280525 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280525 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280525/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280525 Building REAL300000280526 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280526' /scratch/stefan/7769901/working/building/REAL300000280526 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280526 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280526/0 /scratch/stefan/7769901/working/building/REAL300000280526 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/749 `/scratch/stefan/7769901/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1) `REAL300000280526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280526 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 23, 61, 61, 23, 39, 147, 197, 197, 61, 61, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 61, 61, 197, 197, 61, 61, 1] 201 rigid atoms, others: [1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 23] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 654 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280526 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 61, 61, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 6, 22, 22, 1, 1, 61, 61, 61, 61, 61, 61, 112, 112, 112, 112, 112, 1, 1, 22, 22, 1, 1, 61] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 440 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280526 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280526/1 /scratch/stefan/7769901/working/building/REAL300000280526 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/750 `/scratch/stefan/7769901/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1) `REAL300000280526.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280526 none CCC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 5, 5, 5, 13, 37, 37, 13, 28, 107, 192, 192, 37, 37, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 37, 37, 192, 192, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 36] set([0, 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]) total number of confs: 706 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280526 none CCC1=C(S(=O)(=O)NC2=CC=C(OCC#N)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [87, 37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 24, 24, 1, 1, 37, 37, 37, 37, 37, 37, 87, 87, 87, 87, 87, 6, 1, 1, 24, 24, 1, 1, 37] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 399 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280526 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280526 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280526/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280526/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280526 Building REAL300000280527 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280527' /scratch/stefan/7769901/working/building/REAL300000280527 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280527 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280527/0 /scratch/stefan/7769901/working/building/REAL300000280527 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/751 `/scratch/stefan/7769901/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280527 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 29, 29, 25, 26, 88, 88, 88, 88, 93, 93, 29, 29, 7, 7, 7, 1, 1, 1, 1, 3, 3, 29, 29, 88, 88, 88, 29, 29] 114 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280527 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 5, 14, 29, 29, 28, 29, 29, 29, 41, 41, 1, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 29, 29, 28, 29, 41, 41, 1, 1, 7, 7, 7, 1, 1] 114 rigid atoms, others: [36, 37, 41, 42, 11, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280527 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280527 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280527/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280527 Building REAL300000280528 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280528' /scratch/stefan/7769901/working/building/REAL300000280528 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280528 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280528/0 /scratch/stefan/7769901/working/building/REAL300000280528 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/752 `/scratch/stefan/7769901/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000280528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280528 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 1, 1, 1, 1, 3, 3, 35, 35, 35] 48 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280528 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 22, 35, 35, 35, 35, 35, 35, 48, 48, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 22, 22, 35, 35, 35, 35, 48, 48, 1, 1, 1] 48 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280528 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280528 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280528/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280528 Building REAL300000280529 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280529' /scratch/stefan/7769901/working/building/REAL300000280529 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280529 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280529/0 /scratch/stefan/7769901/working/building/REAL300000280529 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/753 `/scratch/stefan/7769901/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280529 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 1, 9, 9, 9, 27, 27, 30, 30, 30, 30, 30, 30, 40, 40, 3, 3, 3, 1, 1, 5, 5, 1, 27, 27, 27, 30, 30, 30, 30, 40, 40] 97 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 34, 13, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280529 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [52, 30, 30, 30, 30, 30, 30, 76, 76, 83, 83, 30, 8, 6, 8, 8, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 52, 52, 52, 30, 30, 76, 76, 30, 6, 6, 6, 1, 1, 1, 1, 3, 3] 97 rigid atoms, others: [38, 39, 40, 41, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 277 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280529 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280529 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280529/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280529 Building REAL300000280530 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280530' /scratch/stefan/7769901/working/building/REAL300000280530 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280530 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280530/0 /scratch/stefan/7769901/working/building/REAL300000280530 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/754 `/scratch/stefan/7769901/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300000280530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280530 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14] 18 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280530 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [11, 6, 11, 14, 14, 14, 14, 14, 14, 18, 18, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 14, 14, 14, 14, 18, 18, 1, 1, 1, 1] 18 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280530 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280530 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280530/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280530 Building REAL300000280531 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280531' /scratch/stefan/7769901/working/building/REAL300000280531 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280531 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280531/0 /scratch/stefan/7769901/working/building/REAL300000280531 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/755 `/scratch/stefan/7769901/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300000280531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280531 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5, 1, 1, 1, 1, 3, 3, 32, 32, 32, 32] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280531 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 8, 22, 32, 32, 32, 32, 32, 32, 45, 45, 1, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 32, 32, 32, 32, 45, 45, 1, 1, 1, 1] 45 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280531 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280531 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280531/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280531 Building REAL300000280532 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280532' /scratch/stefan/7769901/working/building/REAL300000280532 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280532 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280532/0 /scratch/stefan/7769901/working/building/REAL300000280532 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/756 `/scratch/stefan/7769901/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280532 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 51, 51, 51, 51, 51, 51, 58, 58, 3, 3, 3, 1, 1, 1, 24, 24, 24, 51, 51, 51, 51, 58, 58] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280532 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 51, 51, 51, 51, 51, 51, 7, 7, 7, 1, 1, 1, 1, 3, 3] 58 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280532 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280532 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280532/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280532 Building REAL300000280533 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280533' /scratch/stefan/7769901/working/building/REAL300000280533 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280533 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280533/0 /scratch/stefan/7769901/working/building/REAL300000280533 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/757 `/scratch/stefan/7769901/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000280533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280533 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 31, 31, 25, 25, 55, 55, 55, 55, 31, 31, 7, 7, 7, 1, 1, 1, 1, 3, 3, 31, 31, 55, 55, 31, 31] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280533 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 31, 31, 30, 31, 31, 31, 45, 45, 1, 5, 5, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 17, 17, 17, 31, 31, 31, 31, 45, 45, 1, 1, 5, 5, 1, 1] 69 rigid atoms, others: [34, 35, 38, 39, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 170 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280533 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280533 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280533/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280533 Building REAL300000280534 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280534' /scratch/stefan/7769901/working/building/REAL300000280534 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280534 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280534/0 /scratch/stefan/7769901/working/building/REAL300000280534 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/758 `/scratch/stefan/7769901/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280534 none CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 44, 43, 44, 44, 44, 51, 51, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 25, 25, 25, 44, 44, 44, 44, 51, 51, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280534 none CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 44, 44, 44, 45, 45, 44, 44, 44, 44, 44, 5, 5, 5, 1, 1, 1, 1, 3, 3, 44] 51 rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280534 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280534 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280534/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280534 Building REAL300000280535 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280535' /scratch/stefan/7769901/working/building/REAL300000280535 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280535 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280535/0 /scratch/stefan/7769901/working/building/REAL300000280535 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/759 `/scratch/stefan/7769901/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl) `REAL300000280535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280535 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 3, 3, 11, 11, 11] 15 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280535 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 15, 15, 1, 1, 1] 15 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280535 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280535 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280535/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280535 Building REAL300000280536 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280536' /scratch/stefan/7769901/working/building/REAL300000280536 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280536 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280536/0 /scratch/stefan/7769901/working/building/REAL300000280536 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/760 `/scratch/stefan/7769901/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000280536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280536 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 1, 1, 1, 1, 3, 3, 33, 33, 33] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280536 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 9, 24, 33, 33, 33, 33, 33, 33, 43, 43, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 33, 33, 33, 33, 43, 43, 1, 1, 1] 43 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280536 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280536 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280536/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280536 Building REAL300000280537 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280537' /scratch/stefan/7769901/working/building/REAL300000280537 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280537 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280537/0 /scratch/stefan/7769901/working/building/REAL300000280537 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/761 `/scratch/stefan/7769901/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1C) `REAL300000280537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280537 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 9, 11, 11, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 9, 9, 9, 9, 11, 11, 2, 2, 2] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 23, 24, 28, 29] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280537 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 9, 9, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 1, 1, 1, 1, 3, 3, 9, 9, 9] 11 rigid atoms, others: [33, 34, 35, 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, 37, 38, 39, 40, 41]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280537 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280537 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280537/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280537 Building REAL300000280538 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280538' /scratch/stefan/7769901/working/building/REAL300000280538 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280538 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280538/0 /scratch/stefan/7769901/working/building/REAL300000280538 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/762 `/scratch/stefan/7769901/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000280538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280538 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 1, 1, 1, 3, 3, 26, 26, 26] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280538 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 24, 26, 26, 26, 26, 26, 26, 33, 33, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 26, 26, 26, 26, 33, 33, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280538 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280538 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280538/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280538 Building REAL300000280539 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280539' /scratch/stefan/7769901/working/building/REAL300000280539 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280539 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280539/0 /scratch/stefan/7769901/working/building/REAL300000280539 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/763 `/scratch/stefan/7769901/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000280539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280539 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 30, 30, 22, 30, 67, 92, 96, 84, 30, 30, 7, 7, 7, 1, 1, 1, 1, 4, 4, 30, 30, 67, 67, 92, 92, 30, 30] 104 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280539 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 30, 30, 30, 30, 30, 30, 36, 36, 1, 6, 6, 1, 1, 1, 1, 1, 9, 15, 20, 16, 1, 1, 17, 17, 17, 30, 30, 30, 30, 36, 36, 1, 1, 9, 9, 15, 15, 1, 1] 104 rigid atoms, others: [34, 35, 40, 41, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280539 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280539 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280539/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280539 Building REAL300000280540 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280540' /scratch/stefan/7769901/working/building/REAL300000280540 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280540 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280540/0 /scratch/stefan/7769901/working/building/REAL300000280540 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/764 `/scratch/stefan/7769901/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CS1) `REAL300000280540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280540 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 1, 1, 1, 1, 4, 4, 40, 40] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280540 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 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, 8, 27, 40, 40, 39, 40, 40, 40, 49, 49, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 40, 40, 40, 40, 49, 49, 1, 1] 49 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 149 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280540 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280540 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280540/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280540 Building REAL300000280541 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280541' /scratch/stefan/7769901/working/building/REAL300000280541 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280541 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280541/0 /scratch/stefan/7769901/working/building/REAL300000280541 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/765 `/scratch/stefan/7769901/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280541 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 27, 27, 2, 2, 2, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280541 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 27 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280541 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280541 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280541/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280541 Building REAL300000280542 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280542' /scratch/stefan/7769901/working/building/REAL300000280542 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280542 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280542/0 /scratch/stefan/7769901/working/building/REAL300000280542 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/766 `/scratch/stefan/7769901/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000280542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280542 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 25, 25, 11, 20, 95, 176, 178, 178, 25, 25, 5, 5, 5, 1, 1, 1, 1, 3, 3, 25, 25, 176, 176, 25, 25] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 587 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280542 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 5, 16, 25, 25, 24, 25, 25, 25, 37, 37, 1, 5, 5, 1, 1, 1, 1, 1, 6, 28, 42, 42, 1, 1, 17, 17, 17, 25, 25, 24, 25, 37, 37, 1, 1, 28, 28, 1, 1] 200 rigid atoms, others: [34, 35, 38, 39, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 246 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280542 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280542 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280542/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280542 Building REAL300000280543 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280543' /scratch/stefan/7769901/working/building/REAL300000280543 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280543 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280543/0 /scratch/stefan/7769901/working/building/REAL300000280543 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/767 `/scratch/stefan/7769901/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1) `REAL300000280543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280543 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 1, 1, 1, 1, 3, 3, 35, 35, 35, 35, 35] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280543 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 35, 35, 35, 35, 35, 35, 47, 47, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 35, 35, 35, 35, 47, 47, 1, 2, 2, 2, 1] 47 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280543 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280543 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280543/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280543 Building REAL300000280544 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280544' /scratch/stefan/7769901/working/building/REAL300000280544 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280544 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280544/0 /scratch/stefan/7769901/working/building/REAL300000280544 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/768 `/scratch/stefan/7769901/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280544 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 27, 27, 2, 2, 2, 1, 2, 1, 9, 9, 9, 17, 17, 17, 17, 27, 27] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280544 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 34, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 54 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 91 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280544 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280544 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280544/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280544 Building REAL300000280545 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280545' /scratch/stefan/7769901/working/building/REAL300000280545 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280545 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280545/0 /scratch/stefan/7769901/working/building/REAL300000280545 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/769 `/scratch/stefan/7769901/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1) `REAL300000280545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280545 none CC1=C(C(=O)[O-])SC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 8, 8, 8, 28, 28, 42, 42, 41, 42, 42, 42, 50, 50, 1, 2, 2, 2, 29, 29, 29, 42, 42, 42, 42, 50, 50, 1] 50 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 22] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280545 none CC1=C(C(=O)[O-])SC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 16, 6, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 42, 42, 42, 42, 6, 6, 6, 1, 1, 1, 1, 3, 3, 42] 50 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280545 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280545 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280545/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280545 Building REAL300000280546 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280546' /scratch/stefan/7769901/working/building/REAL300000280546 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280546 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280546/0 /scratch/stefan/7769901/working/building/REAL300000280546 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/770 `/scratch/stefan/7769901/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280546 none CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 9, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 1, 2, 2, 2, 7, 7, 7, 9, 9, 9, 9, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280546 none CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 1, 1, 1, 1, 3, 3, 9] 11 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]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280546 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280546 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280546/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280546 Building REAL300000280547 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280547' /scratch/stefan/7769901/working/building/REAL300000280547 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280547 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280547/0 /scratch/stefan/7769901/working/building/REAL300000280547 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/771 `/scratch/stefan/7769901/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CSC(C(=O)[O-])=C1) `REAL300000280547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280547 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 1, 1, 1, 1, 3, 3, 34, 34] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280547 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 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: [25, 9, 25, 34, 34, 34, 34, 34, 34, 46, 46, 1, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 34, 34, 34, 34, 46, 46, 1, 1] 46 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280547 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280547 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280547/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280547 Building REAL300000280548 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280548' /scratch/stefan/7769901/working/building/REAL300000280548 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280548 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280548/0 /scratch/stefan/7769901/working/building/REAL300000280548 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/772 `/scratch/stefan/7769901/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1OC) `REAL300000280548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280548 none COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 4, 3, 3, 3, 1, 11, 11, 11, 13, 13, 13, 13, 13, 13, 1, 5, 5, 5] 17 rigid atoms, others: [1, 2, 3, 4, 5, 40, 19, 20, 21, 24, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280548 none COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 13, 13, 13, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 13, 5, 5, 5, 1, 1, 1, 1, 3, 3, 13, 17, 17, 17] 17 rigid atoms, others: [34, 35, 36, 37, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280548 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280548 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280548/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280548 Building REAL300000280549 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280549' /scratch/stefan/7769901/working/building/REAL300000280549 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280549 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280549/0 /scratch/stefan/7769901/working/building/REAL300000280549 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/773 `/scratch/stefan/7769901/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280549 none COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 69, 69, 69, 69, 69, 69, 81, 81, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 29, 29, 29, 69, 69, 69, 69, 81, 81, 1] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280549 none COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [101, 69, 69, 69, 69, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 69, 69, 69, 99, 99, 101, 101, 101, 69, 69, 5, 5, 5, 1, 1, 1, 1, 3, 3, 69] 109 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280549 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280549 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280549/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280549 Building REAL300000280550 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280550' /scratch/stefan/7769901/working/building/REAL300000280550 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280550 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280550/0 /scratch/stefan/7769901/working/building/REAL300000280550 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/774 `/scratch/stefan/7769901/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2) `REAL300000280550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280550 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 33 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280550 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 6, 9, 9, 9, 9, 9, 9, 11, 11, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 33 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280550 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280550 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280550/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280550 Building REAL300000280551 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280551' /scratch/stefan/7769901/working/building/REAL300000280551 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280551 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280551/0 /scratch/stefan/7769901/working/building/REAL300000280551 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/775 `/scratch/stefan/7769901/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280551 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 13, 13, 13, 13, 13, 13, 15, 15, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 15, 15] 15 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 11, 12, 35, 7] set([0, 2, 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: 50 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280551 none CC(C)C1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 3, 3] 15 rigid atoms, others: [39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 49 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280551 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280551 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280551/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280551 Building REAL300000280552 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280552' /scratch/stefan/7769901/working/building/REAL300000280552 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280552 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280552/0 /scratch/stefan/7769901/working/building/REAL300000280552 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/776 `/scratch/stefan/7769901/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280552 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 11, 11, 25, 25, 25, 25, 25, 25, 35, 35, 6, 6, 6, 6, 6, 1, 1, 1, 11, 11, 11, 25, 25, 25, 25, 35, 35] 35 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280552 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [27, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 3, 3] 35 rigid atoms, others: [36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 89 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280552 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280552 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280552/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280552 Building REAL300000280553 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280553' /scratch/stefan/7769901/working/building/REAL300000280553 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280553 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280553/0 /scratch/stefan/7769901/working/building/REAL300000280553 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/777 `/scratch/stefan/7769901/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280553 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 29, 30] set([7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 26 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280553 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2] 3 rigid atoms, others: [37, 38, 39, 40, 15, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 11 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280553 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280553 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280553/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280553 Building REAL300000280554 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280554' /scratch/stefan/7769901/working/building/REAL300000280554 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280554 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280554/0 /scratch/stefan/7769901/working/building/REAL300000280554 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/778 `/scratch/stefan/7769901/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1) `REAL300000280554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280554 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 19, 19, 19, 19, 19, 13, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 3, 3, 19, 13, 19] 23 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280554 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 5, 12, 19, 19, 18, 19, 19, 19, 23, 23, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 13, 13, 13, 19, 19, 19, 19, 23, 23, 1, 1, 1] 23 rigid atoms, others: [35, 36, 37, 11, 14, 15, 16, 17, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280554 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280554 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280554/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280554 Building REAL300000280555 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280555' /scratch/stefan/7769901/working/building/REAL300000280555 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280555 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280555/0 /scratch/stefan/7769901/working/building/REAL300000280555 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/779 `/scratch/stefan/7769901/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2) `REAL300000280555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280555 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 19 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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, 41, 42]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280555 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 14, 14, 14, 14, 14, 14, 19, 19, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280555 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280555 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280555/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280555 Building REAL300000280556 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280556' /scratch/stefan/7769901/working/building/REAL300000280556 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280556 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280556/0 /scratch/stefan/7769901/working/building/REAL300000280556 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/780 `/scratch/stefan/7769901/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1) `REAL300000280556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280556 none CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 19, 27, 27, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 19, 19, 19, 19, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 19, 17, 18, 35, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280556 none CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 19] 27 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280556 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280556 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280556/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280556 Building REAL300000280557 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280557' /scratch/stefan/7769901/working/building/REAL300000280557 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280557 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280557/0 /scratch/stefan/7769901/working/building/REAL300000280557 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/781 `/scratch/stefan/7769901/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1) `REAL300000280557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280557 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 55, 55, 55, 55, 55, 55, 55, 55, 55, 57, 57, 55, 7, 7, 7, 1, 1, 1, 1, 3, 3, 55, 55, 55, 55, 55, 55] 68 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280557 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 8, 28, 55, 55, 55, 55, 55, 55, 68, 68, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 55, 55, 55, 55, 68, 68, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280557 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280557 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280557/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280557 Building REAL300000280558 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280558' /scratch/stefan/7769901/working/building/REAL300000280558 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280558 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280558/0 /scratch/stefan/7769901/working/building/REAL300000280558 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/782 `/scratch/stefan/7769901/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1) `REAL300000280558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280558 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 9, 9, 9, 23, 23, 36, 36, 36, 36, 36, 36, 38, 38, 1, 2, 2, 2, 1, 2, 23, 23, 23, 36, 36, 36, 36, 38, 38, 1] 76 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 39, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280558 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 36, 36, 36, 36, 36, 72, 5, 5, 5, 1, 1, 1, 1, 3, 3, 36] 76 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280558 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280558 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280558/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280558 Building REAL300000280559 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280559' /scratch/stefan/7769901/working/building/REAL300000280559 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280559 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280559/0 /scratch/stefan/7769901/working/building/REAL300000280559 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/783 `/scratch/stefan/7769901/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1) `REAL300000280559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280559 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 1, 1, 1, 1, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41] 54 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280559 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 8, 26, 41, 41, 40, 41, 41, 41, 54, 54, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 27, 27, 27, 41, 41, 40, 41, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1] 54 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280559 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280559 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280559/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280559 Building REAL300000280560 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280560' /scratch/stefan/7769901/working/building/REAL300000280560 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280560 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280560/0 /scratch/stefan/7769901/working/building/REAL300000280560 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/784 `/scratch/stefan/7769901/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl) `REAL300000280560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280560 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 1, 1, 1, 1, 3, 3, 14, 14] 18 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280560 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 14, 14, 14, 14, 14, 14, 18, 18, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 14, 14, 18, 18, 1, 1] 18 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280560 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280560 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280560/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280560 Building REAL300000280561 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280561' /scratch/stefan/7769901/working/building/REAL300000280561 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280561 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280561/0 /scratch/stefan/7769901/working/building/REAL300000280561 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/785 `/scratch/stefan/7769901/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1) `REAL300000280561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280561 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 7, 7, 35, 35, 17, 17, 113, 199, 199, 199, 35, 35, 35, 5, 5, 5, 1, 1, 1, 1, 3, 3, 35, 35, 199, 199, 35] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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: 646 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280561 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 39, 39, 1, 9, 9, 1, 1, 1, 1, 1, 9, 41, 57, 57, 1, 1, 1, 29, 29, 29, 35, 35, 35, 35, 39, 39, 1, 1, 41, 41, 1] 201 rigid atoms, others: [35, 36, 39, 11, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 298 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280561 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280561 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280561/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280561 Building REAL300000280562 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280562' /scratch/stefan/7769901/working/building/REAL300000280562 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280562 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280562/0 /scratch/stefan/7769901/working/building/REAL300000280562 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/786 `/scratch/stefan/7769901/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1OCC(=O)[O-]) `REAL300000280562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280562 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 44, 43, 44, 44, 44, 44, 44, 1, 1, 1, 1, 7, 41, 66, 66, 2, 2, 2, 1, 25, 25, 25, 44, 44, 44, 44, 44, 44, 1, 1, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 18, 19, 20, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 340 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280562 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 44, 44, 11, 5, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 44, 44, 19, 21, 122, 201, 201, 201, 44, 44, 44, 44, 5, 5, 5, 1, 1, 1, 1, 3, 3, 44, 44, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 678 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280562 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280562 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280562/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280562 Building REAL300000280563 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280563' /scratch/stefan/7769901/working/building/REAL300000280563 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280563 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280563/0 /scratch/stefan/7769901/working/building/REAL300000280563 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/787 `/scratch/stefan/7769901/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280563 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 27, 27, 2, 2, 2, 1, 1, 9, 9, 9, 17, 17, 17, 17, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([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]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280563 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 27 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280563 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280563 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280563/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280563 Building REAL300000280564 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280564' /scratch/stefan/7769901/working/building/REAL300000280564 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280564 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280564/0 /scratch/stefan/7769901/working/building/REAL300000280564 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/788 `/scratch/stefan/7769901/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1) `REAL300000280564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280564 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 7, 7, 36, 36, 34, 36, 151, 199, 199, 199, 36, 36, 36, 5, 5, 5, 1, 1, 1, 1, 3, 3, 36, 36, 199, 199, 36] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280564 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 36, 36, 36, 36, 36, 36, 43, 43, 1, 9, 9, 1, 1, 1, 1, 1, 11, 48, 78, 78, 1, 1, 1, 28, 28, 28, 36, 36, 36, 36, 43, 43, 1, 1, 48, 48, 1] 201 rigid atoms, others: [35, 36, 39, 11, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280564 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280564 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280564/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280564 Building REAL300000280565 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280565' /scratch/stefan/7769901/working/building/REAL300000280565 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280565 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280565/0 /scratch/stefan/7769901/working/building/REAL300000280565 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/789 `/scratch/stefan/7769901/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280565 none CCOC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 19, 19, 19, 19, 19, 19, 25, 25, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 1, 13, 13, 13, 19, 19, 19, 19, 25, 25, 1] 45 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 42, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280565 none CCOC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 19, 19, 19, 19, 11, 5, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 20, 20, 37, 37, 37, 37, 37, 19, 19, 5, 5, 5, 1, 1, 1, 1, 3, 3, 19] 45 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280565 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280565 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280565/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280565 Building REAL300000280566 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280566' /scratch/stefan/7769901/working/building/REAL300000280566 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280566 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280566/0 /scratch/stefan/7769901/working/building/REAL300000280566 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/790 `/scratch/stefan/7769901/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])S1) `REAL300000280566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280566 none CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 19, 28, 28, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 11, 11, 19, 19, 19, 19, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 19, 17, 18, 35, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280566 none CC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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, 19, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 19] 28 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280566 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280566 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280566/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280566 Building REAL300000280567 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280567' /scratch/stefan/7769901/working/building/REAL300000280567 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280567 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280567/0 /scratch/stefan/7769901/working/building/REAL300000280567 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/791 `/scratch/stefan/7769901/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000280567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280567 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 3, 3, 19, 19, 19] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280567 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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, 5, 13, 19, 19, 19, 19, 19, 19, 23, 23, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 19, 19, 19, 19, 23, 23, 1, 1, 1] 23 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280567 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280567 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280567/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280567 Building REAL300000280568 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280568' /scratch/stefan/7769901/working/building/REAL300000280568 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280568 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280568/0 /scratch/stefan/7769901/working/building/REAL300000280568 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/792 `/scratch/stefan/7769901/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000280568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280568 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 1, 1, 1, 1, 3, 3, 35, 35, 35] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280568 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [25, 9, 25, 35, 35, 35, 35, 35, 35, 45, 45, 1, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 25, 25, 25, 35, 35, 35, 35, 45, 45, 1, 1, 1] 45 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280568 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280568 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280568/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280568 Building REAL300000280569 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280569' /scratch/stefan/7769901/working/building/REAL300000280569 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280569 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280569/0 /scratch/stefan/7769901/working/building/REAL300000280569 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/793 `/scratch/stefan/7769901/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])S1) `REAL300000280569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280569 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 1, 1, 1, 1, 4, 4, 30, 30] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280569 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 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: [21, 6, 21, 30, 30, 29, 30, 30, 30, 40, 40, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 30, 30, 30, 30, 40, 40, 1, 1] 40 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 129 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280569 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280569 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280569/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280569 Building REAL300000280570 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280570' /scratch/stefan/7769901/working/building/REAL300000280570 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280570 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280570/0 /scratch/stefan/7769901/working/building/REAL300000280570 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/794 `/scratch/stefan/7769901/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000280570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280570 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 1, 1, 1, 1, 3, 3, 33, 33, 33] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280570 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 33, 33, 33, 33, 33, 33, 45, 45, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 33, 33, 33, 33, 45, 45, 1, 1, 1] 45 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280570 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280570 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280570/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280570 Building REAL300000280571 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280571' /scratch/stefan/7769901/working/building/REAL300000280571 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280571 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280571/0 /scratch/stefan/7769901/working/building/REAL300000280571 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/795 `/scratch/stefan/7769901/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1F) `REAL300000280571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280571 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 1, 9, 9, 9, 25, 25, 35, 35, 35, 35, 35, 35, 43, 43, 1, 1, 2, 2, 2, 1, 1, 25, 25, 25, 35, 35, 35, 35, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280571 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [35, 35, 35, 35, 35, 35, 35, 35, 11, 5, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 1, 1, 1, 1, 3, 3] 43 rigid atoms, others: [33, 34, 35, 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, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280571 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280571 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280571/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280571 Building REAL300000280572 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280572' /scratch/stefan/7769901/working/building/REAL300000280572 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280572 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280572/0 /scratch/stefan/7769901/working/building/REAL300000280572 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/796 `/scratch/stefan/7769901/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C(Cl)C=C1C(=O)[O-]) `REAL300000280572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280572 none COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 35, 35, 35, 35, 35, 35, 44, 44, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 15, 15, 15, 35, 35, 35, 35, 44, 44, 1] 75 rigid atoms, others: [1, 2, 3, 4, 5, 39, 19, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280572 none COC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [66, 35, 35, 35, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 35, 35, 35, 35, 35, 66, 66, 66, 66, 66, 35, 7, 7, 7, 1, 1, 1, 1, 3, 3, 35] 75 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280572 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280572 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280572/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280572 Building REAL300000280573 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280573' /scratch/stefan/7769901/working/building/REAL300000280573 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280573 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280573/0 /scratch/stefan/7769901/working/building/REAL300000280573 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/797 `/scratch/stefan/7769901/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000280573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280573 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 3, 3, 22, 22, 22] 28 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280573 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [15, 8, 15, 22, 22, 22, 22, 22, 22, 28, 28, 1, 8, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 22, 22, 22, 22, 28, 28, 1, 1, 1] 28 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280573 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280573 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280573/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280573 Building REAL300000280574 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280574' /scratch/stefan/7769901/working/building/REAL300000280574 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280574 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280574/0 /scratch/stefan/7769901/working/building/REAL300000280574 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/798 `/scratch/stefan/7769901/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000280574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280574 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 3, 3, 31, 31, 31] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280574 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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] 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: [21, 9, 21, 31, 31, 31, 31, 31, 31, 40, 40, 1, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 31, 31, 31, 31, 40, 40, 1, 1, 1] 40 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280574 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280574 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280574/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280574 Building REAL300000280575 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280575' /scratch/stefan/7769901/working/building/REAL300000280575 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280575 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280575/0 /scratch/stefan/7769901/working/building/REAL300000280575 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/799 `/scratch/stefan/7769901/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280575 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 27, 27, 2, 2, 2, 1, 1, 9, 9, 9, 17, 17, 17, 17, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([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]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280575 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 27 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280575 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280575 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280575/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280575 Building REAL300000280576 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280576' /scratch/stefan/7769901/working/building/REAL300000280576 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280576 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280576/0 /scratch/stefan/7769901/working/building/REAL300000280576 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/800 `/scratch/stefan/7769901/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1) `REAL300000280576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280576 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 19, 19, 16, 17, 119, 119, 191, 199, 199, 199, 19, 19, 5, 5, 5, 1, 1, 1, 1, 3, 3, 19, 19, 191, 191, 199, 199, 19, 19] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 724 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280576 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 18, 19, 19, 19, 25, 25, 1, 5, 5, 1, 1, 1, 1, 1, 12, 12, 53, 66, 74, 74, 1, 1, 15, 15, 15, 19, 19, 18, 19, 25, 25, 1, 1, 53, 53, 66, 66, 1, 1] 201 rigid atoms, others: [43, 36, 37, 42, 11, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 378 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280576 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280576 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280576/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280576 Building REAL300000280577 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280577' /scratch/stefan/7769901/working/building/REAL300000280577 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280577 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280577/0 /scratch/stefan/7769901/working/building/REAL300000280577 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/801 `/scratch/stefan/7769901/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1) `REAL300000280577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280577 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 49, 49, 49, 49, 49, 49, 49, 51, 51, 49, 7, 7, 7, 1, 1, 1, 1, 3, 3, 49, 49] 65 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280577 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 8, 28, 49, 49, 49, 49, 49, 49, 65, 65, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 49, 49, 49, 49, 65, 65, 1, 1] 65 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280577 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280577 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280577/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280577 Building REAL300000280578 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280578' /scratch/stefan/7769901/working/building/REAL300000280578 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280578 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280578/0 /scratch/stefan/7769901/working/building/REAL300000280578 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/802 `/scratch/stefan/7769901/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300000280578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280578 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 1, 1, 1, 1, 3, 3, 33, 33, 33] 41 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280578 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 9, 23, 33, 33, 33, 33, 33, 33, 41, 41, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 33, 33, 33, 33, 41, 41, 1, 1, 1] 41 rigid atoms, others: [35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280578 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280578 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280578/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280578 Building REAL300000280579 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280579' /scratch/stefan/7769901/working/building/REAL300000280579 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280579 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280579/0 /scratch/stefan/7769901/working/building/REAL300000280579 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/803 `/scratch/stefan/7769901/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-]) `REAL300000280579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280579 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 3, 3, 19, 19, 19] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280579 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 17, 19, 19, 19, 19, 19, 19, 19, 19, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280579 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280579/1 /scratch/stefan/7769901/working/building/REAL300000280579 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/804 `/scratch/stefan/7769901/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000280579.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280579 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 3, 3, 23, 23, 23, 46] 54 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280579 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 9, 19, 23, 23, 23, 23, 23, 23, 27, 27, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 23, 23, 23, 23, 27, 27, 1, 1, 1, 2] 54 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 90 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280579 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280579 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280579/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280579/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280579 Building REAL300000280580 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280580' /scratch/stefan/7769901/working/building/REAL300000280580 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280580 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280580/0 /scratch/stefan/7769901/working/building/REAL300000280580 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/805 `/scratch/stefan/7769901/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280580 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 11, 11, 11, 23, 23, 19, 23, 33, 33, 33, 23, 23, 5, 5, 5, 1, 1, 1, 1, 4, 4, 23, 23, 33, 33, 23, 23] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280580 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 17, 23, 23, 23, 23, 23, 23, 27, 27, 1, 6, 6, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 17, 17, 17, 23, 23, 23, 23, 27, 27, 1, 1, 2, 2, 1, 1] 37 rigid atoms, others: [33, 34, 37, 38, 11, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280580 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280580 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280580/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280580 Building REAL300000280581 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280581' /scratch/stefan/7769901/working/building/REAL300000280581 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280581 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280581/0 /scratch/stefan/7769901/working/building/REAL300000280581 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/806 `/scratch/stefan/7769901/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1) `REAL300000280581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280581 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 52, 52, 50, 7, 7, 7, 1, 1, 1, 1, 3, 3, 50, 50] 66 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280581 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 8, 28, 50, 50, 50, 50, 50, 50, 66, 66, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 50, 50, 50, 50, 66, 66, 1, 1] 66 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280581 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280581 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280581/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280581 Building REAL300000280582 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280582' /scratch/stefan/7769901/working/building/REAL300000280582 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280582 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280582/0 /scratch/stefan/7769901/working/building/REAL300000280582 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/807 `/scratch/stefan/7769901/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280582 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 18, 18, 2, 2, 2, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 27, 28, 29] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 56 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280582 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 18 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280582 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280582 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280582/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280582 Building REAL300000280583 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280583' /scratch/stefan/7769901/working/building/REAL300000280583 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280583 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280583/0 /scratch/stefan/7769901/working/building/REAL300000280583 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/808 `/scratch/stefan/7769901/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1F) `REAL300000280583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280583 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 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, 8, 8, 8, 28, 28, 69, 69, 68, 69, 69, 69, 81, 81, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 29, 29, 29, 69, 69, 69, 69, 81, 81, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 38, 18, 19, 20, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280583 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 69, 69, 69, 71, 71, 69, 69, 69, 69, 69, 69, 5, 5, 5, 1, 1, 1, 1, 3, 3, 69] 81 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280583 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280583 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280583/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280583 Building REAL300000280584 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280584' /scratch/stefan/7769901/working/building/REAL300000280584 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280584 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280584/0 /scratch/stefan/7769901/working/building/REAL300000280584 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/809 `/scratch/stefan/7769901/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280584 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 25, 25, 2, 2, 2, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280584 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 25 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280584 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280584 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280584/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280584 Building REAL300000280585 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280585' /scratch/stefan/7769901/working/building/REAL300000280585 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280585 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280585/0 /scratch/stefan/7769901/working/building/REAL300000280585 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/810 `/scratch/stefan/7769901/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1C) `REAL300000280585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280585 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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, 8, 8, 8, 28, 28, 38, 38, 37, 38, 38, 38, 44, 44, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 29, 29, 29, 38, 38, 37, 38, 44, 44, 1, 2, 2, 2] 44 rigid atoms, others: [0, 1, 2, 3, 4, 38, 18, 19, 20, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280585 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [38, 38, 38, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 1, 1, 1, 1, 3, 3, 38, 38, 38, 38] 44 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 92 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280585 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280585 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280585/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280585 Building REAL300000280586 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280586' /scratch/stefan/7769901/working/building/REAL300000280586 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280586 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280586/0 /scratch/stefan/7769901/working/building/REAL300000280586 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/811 `/scratch/stefan/7769901/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1) `REAL300000280586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280586 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5, 1, 1, 1, 1, 3, 3, 32, 32, 32] 43 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280586 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 9, 24, 32, 32, 32, 32, 32, 32, 43, 43, 1, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 24, 24, 24, 32, 32, 32, 32, 43, 43, 1, 1, 1] 43 rigid atoms, others: [35, 36, 37, 11, 14, 15, 16, 17, 18, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280586 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280586 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280586/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280586 Building REAL300000280587 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280587' /scratch/stefan/7769901/working/building/REAL300000280587 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280587 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280587/0 /scratch/stefan/7769901/working/building/REAL300000280587 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/812 `/scratch/stefan/7769901/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F) `REAL300000280587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280587 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 1, 1, 1, 3, 3, 26, 26] 34 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280587 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 26, 26, 26, 26, 26, 26, 34, 34, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 26, 26, 26, 26, 34, 34, 1, 1] 34 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280587 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280587 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280587/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280587 Building REAL300000280588 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280588' /scratch/stefan/7769901/working/building/REAL300000280588 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280588 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280588/0 /scratch/stefan/7769901/working/building/REAL300000280588 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/813 `/scratch/stefan/7769901/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1C(=O)[O-]) `REAL300000280588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280588 none CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280588 none CC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3, 17, 17, 17] 17 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 57 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280588 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280588 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280588/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280588 Building REAL300000280589 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280589' /scratch/stefan/7769901/working/building/REAL300000280589 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280589 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280589/0 /scratch/stefan/7769901/working/building/REAL300000280589 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/814 `/scratch/stefan/7769901/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280589 none CC1=CC(F)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 58, 58, 58, 58, 58, 58, 70, 70, 1, 1, 1, 3, 3, 2, 2, 2, 1, 27, 27, 27, 58, 58, 58, 58, 70, 70, 1] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280589 none CC1=CC(F)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [58, 58, 58, 58, 58, 16, 6, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 58, 58, 58, 58, 58, 58, 58, 58, 58, 6, 6, 6, 1, 1, 1, 1, 3, 3, 58] 70 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280589 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280589 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280589/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280589 Building REAL300000280590 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280590' /scratch/stefan/7769901/working/building/REAL300000280590 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280590 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280590/0 /scratch/stefan/7769901/working/building/REAL300000280590 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/815 `/scratch/stefan/7769901/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1Cl) `REAL300000280590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280590 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 23, 27, 27, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 23, 23, 23, 23, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280590 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [23, 23, 23, 23, 23, 23, 23, 23, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 3, 3] 27 rigid atoms, others: [33, 34, 35, 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, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280590 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280590 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280590/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280590 Building REAL300000280591 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280591' /scratch/stefan/7769901/working/building/REAL300000280591 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280591 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280591/0 /scratch/stefan/7769901/working/building/REAL300000280591 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/816 `/scratch/stefan/7769901/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1) `REAL300000280591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280591 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 9, 9, 9, 29, 29, 63, 63, 63, 63, 63, 63, 70, 70, 1, 2, 2, 2, 1, 29, 29, 29, 63, 63, 63, 63, 70, 70, 1] 70 rigid atoms, others: [0, 1, 2, 3, 4, 38, 7, 8, 9, 10, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280591 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 63, 63, 63, 63, 63, 5, 5, 5, 1, 1, 1, 1, 3, 3, 63] 70 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280591 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280591 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280591/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280591 Building REAL300000280592 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280592' /scratch/stefan/7769901/working/building/REAL300000280592 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280592 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280592/0 /scratch/stefan/7769901/working/building/REAL300000280592 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/817 `/scratch/stefan/7769901/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280592 none CCC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 9, 9, 8, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1, 9, 9, 9, 9, 9, 8, 9, 9, 9, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280592 none CCC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 9, 5, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 9, 9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 9] 17 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]) total number of confs: 79 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280592 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280592 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280592/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280592 Building REAL300000280593 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280593' /scratch/stefan/7769901/working/building/REAL300000280593 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280593 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280593/0 /scratch/stefan/7769901/working/building/REAL300000280593 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/818 `/scratch/stefan/7769901/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1CC(=O)[O-]) `REAL300000280593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280593 none COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 3, 4, 4, 3, 3, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 3, 3] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 36 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280593 none COC1=CC=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 6, 6, 5, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 2, 2, 6, 6, 6] 6 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: 30 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280593 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280593 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280593/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280593 Building REAL300000280594 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280594' /scratch/stefan/7769901/working/building/REAL300000280594 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280594 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280594/0 /scratch/stefan/7769901/working/building/REAL300000280594 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/819 `/scratch/stefan/7769901/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280594 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 21, 21, 2, 2, 2, 1, 1, 9, 9, 9, 17, 17, 17, 17, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 28, 29] set([4, 5, 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]) total number of confs: 68 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280594 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 3, 3] 21 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 57 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280594 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280594 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280594/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280594 Building REAL300000280595 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280595' /scratch/stefan/7769901/working/building/REAL300000280595 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280595 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280595/0 /scratch/stefan/7769901/working/building/REAL300000280595 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/820 `/scratch/stefan/7769901/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1Cl) `REAL300000280595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280595 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 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, 8, 8, 8, 28, 28, 49, 49, 48, 49, 49, 49, 57, 57, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 29, 29, 29, 49, 49, 49, 49, 57, 57, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 38, 18, 19, 20, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280595 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 49, 49, 49, 51, 51, 49, 49, 49, 49, 49, 49, 5, 5, 5, 1, 1, 1, 1, 3, 3, 49] 57 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280595 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280595 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280595/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280595 Building REAL300000280596 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280596' /scratch/stefan/7769901/working/building/REAL300000280596 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280596 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280596/0 /scratch/stefan/7769901/working/building/REAL300000280596 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/821 `/scratch/stefan/7769901/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280596 none CCN1C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 54, 54, 54, 54, 54, 54, 64, 64, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 1, 29, 29, 29, 54, 54, 54, 54, 64, 64, 1] 106 rigid atoms, others: [1, 2, 3, 4, 5, 39, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280596 none CCN1C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [91, 54, 54, 54, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 54, 54, 54, 54, 54, 91, 91, 91, 91, 91, 54, 5, 5, 5, 1, 1, 1, 1, 3, 3, 54] 106 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280596 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280596 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280596/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280596 Building REAL300000280597 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280597' /scratch/stefan/7769901/working/building/REAL300000280597 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280597 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280597/0 /scratch/stefan/7769901/working/building/REAL300000280597 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/822 `/scratch/stefan/7769901/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1CC(=O)[O-]) `REAL300000280597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280597 none CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 9, 10, 10, 1, 1, 1, 1, 3, 5, 5, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 9, 9, 9, 9, 10, 10, 2, 2, 2, 3, 3] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280597 none CC1=CC(C)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 6, 9, 9, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 3, 3, 9, 9, 9, 15, 15] 16 rigid atoms, others: [37, 38, 39, 40, 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, 36, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280597 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280597 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280597/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280597 Building REAL300000280598 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280598' /scratch/stefan/7769901/working/building/REAL300000280598 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280598 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280598/0 /scratch/stefan/7769901/working/building/REAL300000280598 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/823 `/scratch/stefan/7769901/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280598 none CC1=C(Cl)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 70, 70, 69, 70, 70, 70, 80, 80, 1, 1, 1, 3, 3, 2, 2, 2, 1, 29, 29, 29, 70, 70, 69, 70, 80, 80, 1] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280598 none CC1=C(Cl)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [70, 70, 70, 70, 70, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 70, 70, 70, 72, 72, 70, 70, 70, 70, 5, 5, 5, 1, 1, 1, 1, 3, 3, 70] 80 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280598 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280598 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280598/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280598 Building REAL300000280599 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280599' /scratch/stefan/7769901/working/building/REAL300000280599 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280599 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280599/0 /scratch/stefan/7769901/working/building/REAL300000280599 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/824 `/scratch/stefan/7769901/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(C(C)(C)C)SC(C(=O)[O-])=C1) `REAL300000280599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280599 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(C(C)(C)C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 5, 5, 5, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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, 41, 42, 43, 44]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280599 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(C(C)(C)C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 5, 5, 5, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 2, 2, 2, 2, 3, 3, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [11, 44, 14, 15, 16, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280599 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280599 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280599/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280599 Building REAL300000280600 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280600' /scratch/stefan/7769901/working/building/REAL300000280600 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280600 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280600/0 /scratch/stefan/7769901/working/building/REAL300000280600 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/825 `/scratch/stefan/7769901/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280600 none COC1=CC(Cl)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 37, 37, 37, 37, 37, 37, 43, 43, 1, 1, 1, 3, 3, 3, 3, 3, 1, 19, 19, 19, 37, 37, 37, 37, 43, 43, 1] 77 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280600 none COC1=CC(Cl)=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [67, 37, 37, 37, 37, 37, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 37, 37, 37, 67, 67, 67, 67, 67, 37, 7, 7, 7, 1, 1, 1, 1, 4, 4, 37] 77 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280600 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280600 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280600/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280600 Building REAL300000280601 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280601' /scratch/stefan/7769901/working/building/REAL300000280601 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280601 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280601/0 /scratch/stefan/7769901/working/building/REAL300000280601 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/826 `/scratch/stefan/7769901/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1C(=O)[O-]) `REAL300000280601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280601 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 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, 9, 22, 22, 42, 42, 42, 42, 42, 42, 50, 50, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 22, 22, 22, 42, 42, 42, 42, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 18, 19, 20, 21, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280601 none CC1=CC(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 1, 1, 1, 1, 3, 3, 42, 42] 50 rigid atoms, others: [32, 33, 34, 7, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280601 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280601 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280601/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280601 Building REAL300000280602 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280602' /scratch/stefan/7769901/working/building/REAL300000280602 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280602 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280602/0 /scratch/stefan/7769901/working/building/REAL300000280602 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/827 `/scratch/stefan/7769901/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-]) `REAL300000280602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280602 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 9, 9, 9, 9, 9, 7, 7, 7, 1, 1, 1, 1, 3, 3, 9, 9, 16, 16, 9] 16 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280602 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 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] 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, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 1, 5, 5, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 7, 7, 7, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1] 16 rigid atoms, others: [36, 37, 40, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280602 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280602 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280602/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280602 Building REAL300000280603 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280603' /scratch/stefan/7769901/working/building/REAL300000280603 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280603 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280603/0 /scratch/stefan/7769901/working/building/REAL300000280603 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/828 `/scratch/stefan/7769901/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280603 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 3, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 33, 33, 2, 2, 2, 1, 1, 9, 9, 9, 23, 23, 23, 23, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280603 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 23, 23, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 3, 3] 33 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 73 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280603 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280603 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280603/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280603 Building REAL300000280604 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280604' /scratch/stefan/7769901/working/building/REAL300000280604 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280604 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280604/0 /scratch/stefan/7769901/working/building/REAL300000280604 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/829 `/scratch/stefan/7769901/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-]) `REAL300000280604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280604 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 3, 3, 7, 7, 7] 8 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280604 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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: [7, 5, 7, 7, 7, 7, 7, 7, 7, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 8, 8, 1, 1, 1] 8 rigid atoms, others: [35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280604 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280604 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280604/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280604 Building REAL300000280605 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280605' /scratch/stefan/7769901/working/building/REAL300000280605 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280605 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280605/0 /scratch/stefan/7769901/working/building/REAL300000280605 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/830 `/scratch/stefan/7769901/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000280605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280605 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 3, 3, 30, 30, 30] 34 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280605 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 9, 19, 30, 30, 30, 30, 30, 30, 34, 34, 1, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 19, 19, 19, 30, 30, 30, 30, 34, 34, 1, 1, 1] 34 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280605 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280605 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280605/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280605 Building REAL300000280606 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280606' /scratch/stefan/7769901/working/building/REAL300000280606 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280606 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280606/0 /scratch/stefan/7769901/working/building/REAL300000280606 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/831 `/scratch/stefan/7769901/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-]) `REAL300000280606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280606 none CC1=C(F)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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, 8, 8, 8, 28, 28, 67, 67, 66, 67, 67, 67, 77, 77, 1, 1, 1, 3, 3, 2, 2, 2, 1, 29, 29, 29, 67, 67, 67, 67, 77, 77, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280606 none CC1=C(F)C=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 2, 2, 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: [67, 67, 67, 67, 67, 15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 67, 67, 67, 69, 69, 67, 67, 67, 67, 5, 5, 5, 1, 1, 1, 1, 3, 3, 67] 77 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280606 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280606 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280606/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280606 Building REAL300000280607 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280607' /scratch/stefan/7769901/working/building/REAL300000280607 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280607 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280607/0 /scratch/stefan/7769901/working/building/REAL300000280607 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/832 `/scratch/stefan/7769901/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1) `REAL300000280607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280607 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 39, 5, 5, 5, 1, 1, 1, 1, 3, 3, 39, 39, 39, 39, 39, 39] 51 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280607 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 8, 26, 39, 39, 39, 39, 39, 39, 51, 51, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 39, 39, 39, 39, 51, 51, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280607 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280607 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280607/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280607 Building REAL300000280608 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280608' /scratch/stefan/7769901/working/building/REAL300000280608 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280608 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280608/0 /scratch/stefan/7769901/working/building/REAL300000280608 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/833 `/scratch/stefan/7769901/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300000280608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280608 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 1, 1, 1, 1, 3, 3, 37, 37, 37] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280608 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [25, 9, 25, 37, 37, 37, 37, 37, 37, 53, 53, 1, 9, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 37, 37, 37, 37, 53, 53, 1, 1, 1] 53 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280608 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280608 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280608/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280608 Building REAL300000280609 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280609' /scratch/stefan/7769901/working/building/REAL300000280609 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280609 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280609/0 /scratch/stefan/7769901/working/building/REAL300000280609 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/834 `/scratch/stefan/7769901/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O) `REAL300000280609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280609 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 41, 41, 41, 41, 41, 41, 49, 49, 4, 4, 4, 1, 1, 1, 25, 25, 25, 41, 41, 41, 41, 49, 49] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280609 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)N(C)C1=CC=CC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 41, 41, 41, 41, 5, 5, 5, 1, 1, 1, 1, 3, 3] 49 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280609 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280609 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280609/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280609 Building REAL300000280610 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280610' /scratch/stefan/7769901/working/building/REAL300000280610 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280610 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280610/0 /scratch/stefan/7769901/working/building/REAL300000280610 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/835 `/scratch/stefan/7769901/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000280610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280610 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 1, 1, 1, 1, 3, 3, 27] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280610 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 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: [17, 7, 17, 27, 27, 27, 27, 27, 27, 39, 39, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 27, 27, 27, 27, 39, 39, 1] 39 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280610 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280610 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280610/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280610 Building REAL300000280611 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280611' /scratch/stefan/7769901/working/building/REAL300000280611 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280611 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280611/0 /scratch/stefan/7769901/working/building/REAL300000280611 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/836 `/scratch/stefan/7769901/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1) `REAL300000280611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280611 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 19, 38, 40, 40, 40, 40, 40, 40, 44, 44, 1, 19, 19, 1, 9, 9, 1, 1, 1, 3, 3, 1, 1, 9, 9, 38, 38, 38, 40, 40, 40, 40, 44, 44, 9, 9, 1, 1, 1, 1, 9, 9] 44 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 173 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280611 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 22, 22, 18, 18, 40, 40, 40, 40, 40, 22, 22, 5, 5, 5, 1, 1, 1, 1, 3, 3, 22, 22, 40, 40, 40, 40, 22, 22] 44 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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, 41, 42]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280611 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 5, 15, 22, 22, 21, 22, 22, 22, 26, 26, 1, 5, 5, 1, 1, 1, 1, 1, 9, 12, 12, 9, 9, 1, 1, 16, 16, 16, 22, 22, 21, 22, 26, 26, 1, 1, 9, 9, 9, 9, 1, 1] 44 rigid atoms, others: [35, 36, 41, 42, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280611 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280611 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280611/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280611 Building REAL300000280612 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280612' /scratch/stefan/7769901/working/building/REAL300000280612 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280612 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280612/0 /scratch/stefan/7769901/working/building/REAL300000280612 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/837 `/scratch/stefan/7769901/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2CC(C(=O)[O-])CC2=C1) `REAL300000280612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280612 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2CC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 1, 1, 1, 3, 3, 26, 26, 26, 26, 26, 26, 26, 26] 32 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 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, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280612 none CN(C1=CC=CC=C1C(N)=O)S(=O)(=O)C1=CC=C2CC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 1, 1, 1, 1, 1, 1, 8, 11, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 21, 26, 26, 26, 26, 26, 26, 32, 32, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 26, 26, 26, 26, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280612 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280612 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280612/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280612 Building REAL300000280613 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280613' /scratch/stefan/7769901/working/building/REAL300000280613 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280613 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280613/0 /scratch/stefan/7769901/working/building/REAL300000280613 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/838 `/scratch/stefan/7769901/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1) `REAL300000280613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280613 none CCC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 21, 21, 21, 21, 21, 21, 29, 29, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 21, 21, 21, 21, 29, 29, 1] 29 rigid atoms, others: [1, 2, 3, 4, 38, 18, 19, 20, 21, 22, 23] set([0, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280613 none CCC1=C(S(=O)(=O)N(C)C2=CC=CC=C2C(N)=O)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 5, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 3, 3, 21] 29 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280613 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280613 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280613/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280613 Building REAL300000280614 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280614' /scratch/stefan/7769901/working/building/REAL300000280614 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280614 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280614/0 /scratch/stefan/7769901/working/building/REAL300000280614 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/839 `/scratch/stefan/7769901/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000280614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280614 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 69, 69, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37] 135 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280614 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 37, 37, 37, 37, 37, 37, 85, 85, 85, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 37, 37, 85, 85, 85, 85, 37, 1, 1, 1] 135 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280614 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280614/1 /scratch/stefan/7769901/working/building/REAL300000280614 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/840 `/scratch/stefan/7769901/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000280614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280614 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 67, 67, 37, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 37, 37, 37] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280614 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [67, 37, 37, 37, 37, 37, 37, 77, 77, 77, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 67, 67, 37, 37, 77, 77, 77, 77, 37, 9, 1, 1, 1] 121 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280614 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280614 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280614/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280614/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280614 Building REAL300000280615 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280615' /scratch/stefan/7769901/working/building/REAL300000280615 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280615 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280615/0 /scratch/stefan/7769901/working/building/REAL300000280615 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/841 `/scratch/stefan/7769901/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300000280615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280615 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 19, 19, 19, 19] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280615 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 19, 19, 19, 19, 19, 19, 53, 53, 53, 19, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 19, 19, 53, 53, 53, 53, 19, 1, 1, 1, 1] 53 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280615 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280615/1 /scratch/stefan/7769901/working/building/REAL300000280615 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/842 `/scratch/stefan/7769901/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300000280615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280615 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 9, 21, 21, 21, 21] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280615 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 21, 21, 21, 21, 21, 21, 53, 53, 53, 21, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 21, 21, 53, 53, 53, 53, 21, 5, 1, 1, 1, 1] 53 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280615 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280615 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280615/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280615/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280615 Building REAL300000280616 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280616' /scratch/stefan/7769901/working/building/REAL300000280616 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280616 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280616/0 /scratch/stefan/7769901/working/building/REAL300000280616 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/843 `/scratch/stefan/7769901/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300000280616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280616 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 39, 39, 39, 39] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280616 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 39, 39, 39, 39, 39, 39, 93, 93, 93, 39, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 39, 39, 93, 93, 93, 93, 39, 1, 1, 1, 1] 93 rigid atoms, others: [35, 36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280616 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280616/1 /scratch/stefan/7769901/working/building/REAL300000280616 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/844 `/scratch/stefan/7769901/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300000280616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280616 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 37, 37, 37, 37] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280616 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [41, 37, 37, 37, 37, 37, 37, 87, 87, 87, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 37, 37, 87, 87, 87, 87, 37, 9, 1, 1, 1, 1] 87 rigid atoms, others: [36, 37, 38, 39, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280616 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280616 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280616/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280616/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280616 Building REAL300000280617 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280617' /scratch/stefan/7769901/working/building/REAL300000280617 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280617 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280617/0 /scratch/stefan/7769901/working/building/REAL300000280617 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/845 `/scratch/stefan/7769901/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC) `REAL300000280617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280617 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 83, 83, 83, 83, 83, 83, 83, 83, 83, 118, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 83, 83, 83, 118, 118, 118] 190 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280617 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [126, 83, 83, 83, 83, 83, 83, 153, 153, 153, 83, 23, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 126, 126, 126, 83, 83, 153, 153, 153, 153, 83, 1, 1, 1, 4, 4, 4] 190 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280617 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280617 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280617/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280617 Building REAL300000280618 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280618' /scratch/stefan/7769901/working/building/REAL300000280618 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280618 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280618/0 /scratch/stefan/7769901/working/building/REAL300000280618 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/846 `/scratch/stefan/7769901/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000280618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280618 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 55, 55, 65, 65, 17, 17, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 17, 17, 55, 55, 17, 17] 125 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280618 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 17, 17, 17, 17, 17, 17, 39, 39, 39, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 1, 1, 29, 29, 29, 17, 17, 39, 39, 39, 39, 17, 1, 1, 5, 5, 1, 1] 125 rigid atoms, others: [37, 38, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 140 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280618 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280618/1 /scratch/stefan/7769901/working/building/REAL300000280618 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/847 `/scratch/stefan/7769901/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000280618.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280618 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 56, 56, 72, 72, 17, 17, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 7, 17, 17, 56, 56, 17, 17] 133 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280618 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 17, 17, 17, 17, 17, 17, 39, 39, 39, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 11, 11, 1, 1, 31, 31, 31, 17, 17, 39, 39, 39, 39, 17, 5, 1, 1, 5, 5, 1, 1] 133 rigid atoms, others: [38, 39, 42, 43, 13, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280618 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280618 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280618/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280618/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280618 Building REAL300000280619 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280619' /scratch/stefan/7769901/working/building/REAL300000280619 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280619 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280619/0 /scratch/stefan/7769901/working/building/REAL300000280619 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/848 `/scratch/stefan/7769901/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1) `REAL300000280619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280619 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37, 37] 74 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280619 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 37, 37, 37, 74, 74, 74, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 37, 37, 37, 37, 74, 74, 74, 74, 37, 1, 1, 2, 2, 2, 1] 74 rigid atoms, others: [36, 37, 41, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280619 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280619/1 /scratch/stefan/7769901/working/building/REAL300000280619 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/849 `/scratch/stefan/7769901/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1) `REAL300000280619.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280619 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 7, 34, 34, 34, 34, 34, 34] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280619 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 34, 34, 34, 34, 34, 34, 60, 60, 60, 34, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 34, 34, 60, 60, 60, 60, 34, 9, 1, 1, 2, 2, 2, 1] 60 rigid atoms, others: [37, 38, 42, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280619 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280619 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280619/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280619/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280619 Building REAL300000280620 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280620' /scratch/stefan/7769901/working/building/REAL300000280620 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280620 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280620/0 /scratch/stefan/7769901/working/building/REAL300000280620 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/850 `/scratch/stefan/7769901/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl) `REAL300000280620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280620 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 32, 32, 32] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280620 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 32, 32, 32, 32, 32, 32, 58, 58, 58, 32, 11, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 39, 39, 39, 32, 32, 58, 58, 58, 58, 32, 1, 1, 1] 58 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280620 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280620 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280620/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280620 Building REAL300000280621 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280621' /scratch/stefan/7769901/working/building/REAL300000280621 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280621 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280621/0 /scratch/stefan/7769901/working/building/REAL300000280621 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/851 `/scratch/stefan/7769901/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000280621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280621 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37] 77 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280621 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 37, 37, 37, 77, 77, 77, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 37, 37, 37, 37, 77, 77, 77, 77, 37, 1, 1, 1] 77 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280621 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280621/1 /scratch/stefan/7769901/working/building/REAL300000280621 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/852 `/scratch/stefan/7769901/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000280621.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280621 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 35, 35, 35, 35, 35, 35, 39, 39, 35, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 35, 35, 35] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280621 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [41, 35, 35, 35, 35, 35, 35, 66, 66, 66, 35, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 41, 35, 35, 66, 66, 66, 66, 35, 9, 1, 1, 1] 70 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280621 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280621 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280621/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280621/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280621 Building REAL300000280622 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280622' /scratch/stefan/7769901/working/building/REAL300000280622 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280622 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280622/0 /scratch/stefan/7769901/working/building/REAL300000280622 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/853 `/scratch/stefan/7769901/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C) `REAL300000280622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280622 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 39, 39, 39, 39, 39, 39, 39, 39] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280622 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 39, 39, 39, 39, 39, 39, 63, 63, 63, 39, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 39, 39, 63, 63, 63, 63, 39, 1, 1, 2, 2, 2, 2, 2, 2] 63 rigid atoms, others: [37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280622 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280622/1 /scratch/stefan/7769901/working/building/REAL300000280622 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/854 `/scratch/stefan/7769901/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C) `REAL300000280622.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280622 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 8, 42, 42, 42, 42, 42, 42, 42, 42] 68 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 135 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280622 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [46, 42, 42, 42, 42, 42, 42, 68, 68, 68, 42, 12, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 42, 42, 68, 68, 68, 68, 42, 12, 1, 1, 2, 2, 2, 2, 2, 2] 68 rigid atoms, others: [38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280622 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280622 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280622/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280622/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280622 Building REAL300000280623 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280623' /scratch/stefan/7769901/working/building/REAL300000280623 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280623 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280623/0 /scratch/stefan/7769901/working/building/REAL300000280623 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/855 `/scratch/stefan/7769901/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000280623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280623 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 75, 75, 75, 75, 75, 75, 75, 75, 75, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 75, 75, 75] 136 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280623 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 75, 75, 75, 75, 75, 75, 136, 136, 136, 75, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 82, 82, 82, 75, 75, 136, 136, 136, 136, 75, 1, 1, 1] 136 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280623 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280623 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280623/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280623 Building REAL300000280624 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280624' /scratch/stefan/7769901/working/building/REAL300000280624 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280624 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280624/0 /scratch/stefan/7769901/working/building/REAL300000280624 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/856 `/scratch/stefan/7769901/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000280624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280624 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 26, 44, 44, 44, 12, 12, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 12, 12, 26, 26, 44, 44, 12, 12] 85 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280624 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 12, 12, 12, 12, 12, 12, 28, 28, 28, 12, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 18, 18, 18, 12, 12, 28, 28, 28, 28, 12, 1, 1, 4, 4, 7, 7, 1, 1] 85 rigid atoms, others: [37, 38, 43, 44, 13, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280624 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280624/1 /scratch/stefan/7769901/working/building/REAL300000280624 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/857 `/scratch/stefan/7769901/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000280624.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280624 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 27, 63, 73, 73, 14, 14, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 6, 14, 14, 27, 27, 63, 63, 14, 14] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280624 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 14, 14, 14, 14, 14, 14, 26, 26, 26, 14, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 8, 11, 11, 1, 1, 22, 22, 22, 14, 14, 26, 26, 26, 26, 14, 5, 1, 1, 4, 4, 8, 8, 1, 1] 93 rigid atoms, others: [38, 39, 44, 13, 45, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280624 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280624 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280624/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280624/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280624 Building REAL300000280625 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280625' /scratch/stefan/7769901/working/building/REAL300000280625 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280625 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280625/0 /scratch/stefan/7769901/working/building/REAL300000280625 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/858 `/scratch/stefan/7769901/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1) `REAL300000280625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280625 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 79, 79, 79, 79, 79, 79, 79, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 79, 79] 171 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 27, 28] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280625 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [88, 79, 79, 79, 79, 79, 79, 171, 171, 171, 79, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 79, 79, 171, 171, 171, 171, 79, 1, 1] 171 rigid atoms, others: [34, 35, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 448 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280625 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280625 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280625/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280625 Building REAL300000280626 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280626' /scratch/stefan/7769901/working/building/REAL300000280626 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280626 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280626/0 /scratch/stefan/7769901/working/building/REAL300000280626 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/859 `/scratch/stefan/7769901/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000280626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280626 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37, 37] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280626 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 37, 37, 37, 60, 60, 60, 37, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 60, 60, 60, 60, 37, 1, 1, 1, 2, 2, 2] 60 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280626 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280626/1 /scratch/stefan/7769901/working/building/REAL300000280626 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/860 `/scratch/stefan/7769901/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000280626.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280626 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 8, 43, 43, 43, 43, 43, 43] 71 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280626 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [49, 43, 43, 43, 43, 43, 43, 71, 71, 71, 43, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 43, 43, 71, 71, 71, 71, 43, 13, 1, 1, 1, 2, 2, 2] 71 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280626 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280626 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280626/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280626/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280626 Building REAL300000280627 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280627' /scratch/stefan/7769901/working/building/REAL300000280627 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280627 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280627/0 /scratch/stefan/7769901/working/building/REAL300000280627 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/861 `/scratch/stefan/7769901/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000280627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280627 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 93, 125, 145, 145, 19, 19, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 19, 19, 125, 125, 19, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 406 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280627 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 19, 19, 19, 19, 19, 19, 47, 47, 47, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 36, 36, 1, 1, 38, 38, 38, 19, 19, 47, 47, 47, 47, 19, 1, 1, 19, 19, 1, 1] 201 rigid atoms, others: [37, 38, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 261 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280627 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280627/1 /scratch/stefan/7769901/working/building/REAL300000280627 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/862 `/scratch/stefan/7769901/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000280627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280627 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 40, 71, 72, 72, 13, 13, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 5, 13, 13, 71, 71, 13, 13] 80 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 252 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280627 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 13, 13, 13, 13, 13, 13, 18, 18, 18, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 19, 26, 26, 1, 1, 16, 16, 16, 13, 13, 18, 18, 18, 18, 13, 5, 1, 1, 19, 19, 1, 1] 80 rigid atoms, others: [38, 39, 42, 43, 13, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 132 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280627 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280627 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280627/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280627/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280627 Building REAL300000280628 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280628' /scratch/stefan/7769901/working/building/REAL300000280628 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280628 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280628/0 /scratch/stefan/7769901/working/building/REAL300000280628 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/863 `/scratch/stefan/7769901/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1) `REAL300000280628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280628 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 41, 41, 41, 41, 41] 101 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280628 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [49, 41, 41, 41, 41, 41, 41, 101, 101, 101, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 49, 49, 41, 41, 101, 101, 101, 101, 41, 1, 2, 2, 2, 1] 101 rigid atoms, others: [35, 39, 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, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280628 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280628 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280628/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280628 Building REAL300000280629 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280629' /scratch/stefan/7769901/working/building/REAL300000280629 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280629 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280629/0 /scratch/stefan/7769901/working/building/REAL300000280629 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/864 `/scratch/stefan/7769901/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C) `REAL300000280629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280629 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 41, 41, 41, 64, 64, 41, 41, 41, 41, 41, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 41, 82, 41, 41, 41, 41] 196 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 295 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280629 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [64, 41, 41, 41, 41, 41, 41, 66, 66, 66, 41, 18, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 64, 64, 64, 41, 41, 66, 66, 66, 66, 41, 1, 2, 1, 2, 2, 2] 196 rigid atoms, others: [37, 39, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 40, 41, 42]) total number of confs: 221 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280629 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280629/1 /scratch/stefan/7769901/working/building/REAL300000280629 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/865 `/scratch/stefan/7769901/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C) `REAL300000280629.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280629 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 208 conformations in input total number of sets (complete confs): 208 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 45, 45, 45, 75, 75, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 8, 45, 90, 45, 45, 45, 45] 208 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280629 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 208 conformations in input total number of sets (complete confs): 208 using faster count positions algorithm for large data unique positions, atoms: [77, 45, 45, 45, 45, 45, 45, 70, 70, 70, 45, 11, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 77, 77, 77, 45, 45, 70, 70, 70, 70, 45, 11, 1, 2, 1, 2, 2, 2] 208 rigid atoms, others: [38, 40, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280629 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280629 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280629/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280629/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280629 Building REAL300000280630 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280630' /scratch/stefan/7769901/working/building/REAL300000280630 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280630 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280630/0 /scratch/stefan/7769901/working/building/REAL300000280630 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/866 `/scratch/stefan/7769901/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1) `REAL300000280630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280630 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 22, 22, 22, 80, 80, 80, 80, 80, 108, 108, 80, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 80, 80, 80, 80] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280630 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 80, 80, 80, 80, 80, 80, 169, 169, 169, 80, 24, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 114, 114, 114, 80, 80, 169, 169, 169, 169, 80, 1, 2, 2, 2] 201 rigid atoms, others: [35, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280630 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280630 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280630/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280630 Building REAL300000280631 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280631' /scratch/stefan/7769901/working/building/REAL300000280631 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280631 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280631/0 /scratch/stefan/7769901/working/building/REAL300000280631 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/867 `/scratch/stefan/7769901/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C) `REAL300000280631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280631 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 35, 35, 35, 55, 55, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 35, 35, 35, 35, 35, 35, 35, 35] 83 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280631 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 35, 35, 35, 35, 35, 35, 57, 57, 57, 35, 13, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 55, 55, 55, 35, 35, 57, 57, 57, 57, 35, 1, 2, 2, 2, 1, 2, 2, 2] 83 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 42, 43, 44]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280631 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280631/1 /scratch/stefan/7769901/working/building/REAL300000280631 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/868 `/scratch/stefan/7769901/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C) `REAL300000280631.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280631 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 45, 45, 45, 75, 75, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 8, 45, 45, 45, 45, 45, 45, 45, 45] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280631 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [75, 45, 45, 45, 45, 45, 45, 62, 62, 62, 45, 11, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 75, 75, 75, 45, 45, 62, 62, 62, 62, 45, 11, 1, 2, 2, 2, 1, 2, 2, 2] 96 rigid atoms, others: [38, 42, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280631 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280631 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280631/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280631/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280631 Building REAL300000280632 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280632' /scratch/stefan/7769901/working/building/REAL300000280632 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280632 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280632/0 /scratch/stefan/7769901/working/building/REAL300000280632 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/869 `/scratch/stefan/7769901/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1) `REAL300000280632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280632 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 41, 41] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 27, 28] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280632 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [43, 41, 41, 41, 41, 41, 41, 99, 99, 99, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 41, 41, 99, 99, 99, 99, 41, 1, 1] 99 rigid atoms, others: [34, 35, 13, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 254 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280632 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280632 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280632/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280632 Building REAL300000280633 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280633' /scratch/stefan/7769901/working/building/REAL300000280633 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280633 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280633/0 /scratch/stefan/7769901/working/building/REAL300000280633 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/870 `/scratch/stefan/7769901/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1) `REAL300000280633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280633 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 69, 37, 37, 67, 67, 37, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 37, 37, 69, 69, 69, 37] 196 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280633 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [71, 37, 37, 37, 37, 37, 37, 76, 76, 76, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 71, 71, 71, 37, 37, 76, 76, 76, 76, 37, 1, 1, 3, 3, 3, 1] 196 rigid atoms, others: [37, 38, 42, 13, 16, 17, 18, 19, 20, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280633 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280633/1 /scratch/stefan/7769901/working/building/REAL300000280633 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/871 `/scratch/stefan/7769901/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1) `REAL300000280633.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280633 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 35, 35, 35, 35, 65, 35, 35, 63, 63, 35, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 7, 35, 35, 65, 65, 65, 35] 165 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280633 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(OC)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [65, 35, 35, 35, 35, 35, 35, 59, 59, 59, 35, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 65, 65, 65, 35, 35, 59, 59, 59, 59, 35, 9, 1, 1, 3, 3, 3, 1] 165 rigid atoms, others: [38, 39, 43, 13, 16, 17, 18, 19, 20, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280633 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280633 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280633/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280633/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280633 Building REAL300000280634 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280634' /scratch/stefan/7769901/working/building/REAL300000280634 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280634 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280634/0 /scratch/stefan/7769901/working/building/REAL300000280634 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/872 `/scratch/stefan/7769901/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC(NC(C)=O)=CC=C1OC) `REAL300000280634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280634 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC(NC(C)=O)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 11, 11, 11, 17, 17, 17, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 17, 17, 17, 17, 11, 11, 11, 11, 11] 17 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 11] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280634 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC(NC(C)=O)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 5, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 13, 13, 13, 13, 13, 11, 11, 11, 1, 4, 4, 4, 4, 1, 1, 3, 3, 3] 17 rigid atoms, others: [35, 40, 41, 14, 15, 16, 17, 18, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280634 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280634/1 /scratch/stefan/7769901/working/building/REAL300000280634 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/873 `/scratch/stefan/7769901/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC(NC(C)=O)=CC=C1OC) `REAL300000280634.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280634 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC(NC(C)=O)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 47, 47, 47, 71, 71, 71, 47, 47, 47, 47, 69, 6, 6, 6, 6, 6, 1, 1, 1, 13, 47, 71, 71, 71, 71, 47, 47, 69, 69, 69] 103 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 34] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280634 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC(NC(C)=O)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 8, 23, 23, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 73, 73, 73, 73, 73, 47, 47, 47, 8, 1, 4, 4, 4, 4, 1, 1, 3, 3, 3] 103 rigid atoms, others: [36, 41, 42, 14, 15, 16, 17, 18, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 280 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280634 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280634 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280634/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280634/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280634 Building REAL300000280635 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280635' /scratch/stefan/7769901/working/building/REAL300000280635 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280635 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280635/0 /scratch/stefan/7769901/working/building/REAL300000280635 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/874 `/scratch/stefan/7769901/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1) `REAL300000280635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280635 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 69, 69, 69, 69, 69, 69, 69, 69, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 69, 69, 69, 69] 151 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280635 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [75, 69, 69, 69, 69, 69, 69, 151, 151, 151, 69, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 75, 69, 69, 151, 151, 151, 151, 69, 2, 2, 2, 1] 151 rigid atoms, others: [38, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280635 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280635 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280635/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280635 Building REAL300000280636 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280636' /scratch/stefan/7769901/working/building/REAL300000280636 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280636 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280636/0 /scratch/stefan/7769901/working/building/REAL300000280636 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/875 `/scratch/stefan/7769901/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O) `REAL300000280636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280636 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 25, 25, 25, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 86, 86, 86, 86, 86, 172] 334 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280636 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [98, 86, 86, 86, 86, 86, 86, 167, 167, 167, 86, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 98, 98, 98, 86, 86, 167, 167, 167, 167, 86, 1, 2, 2, 2, 1, 2] 334 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 42]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280636 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280636 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280636/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280636 Building REAL300000280637 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280637' /scratch/stefan/7769901/working/building/REAL300000280637 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280637 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280637/0 /scratch/stefan/7769901/working/building/REAL300000280637 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/876 `/scratch/stefan/7769901/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C) `REAL300000280637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280637 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 47, 47, 47, 47, 47] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280637 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 47, 47, 47, 47, 47, 47, 75, 75, 75, 47, 21, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 51, 51, 51, 47, 47, 75, 75, 75, 75, 47, 1, 1, 2, 2, 2] 75 rigid atoms, others: [37, 38, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280637 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280637/1 /scratch/stefan/7769901/working/building/REAL300000280637 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/877 `/scratch/stefan/7769901/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C) `REAL300000280637.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280637 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 8, 43, 43, 43, 43, 43] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280637 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [47, 43, 43, 43, 43, 43, 43, 69, 69, 69, 43, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 43, 43, 69, 69, 69, 69, 43, 11, 1, 1, 2, 2, 2] 69 rigid atoms, others: [38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280637 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280637 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280637/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280637/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280637 Building REAL300000280638 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280638' /scratch/stefan/7769901/working/building/REAL300000280638 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280638 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280638/0 /scratch/stefan/7769901/working/building/REAL300000280638 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/878 `/scratch/stefan/7769901/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1) `REAL300000280638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280638 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 59, 59, 59, 59, 59, 59, 59, 59, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 59, 59, 59, 59] 114 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280638 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 59, 59, 59, 59, 59, 59, 114, 114, 114, 59, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 61, 61, 59, 59, 114, 114, 114, 114, 59, 1, 1, 1, 1] 114 rigid atoms, others: [35, 36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280638 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280638 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280638/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280638 Building REAL300000280639 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280639' /scratch/stefan/7769901/working/building/REAL300000280639 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280639 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280639/0 /scratch/stefan/7769901/working/building/REAL300000280639 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/879 `/scratch/stefan/7769901/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000280639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280639 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 35, 35, 21, 31, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 35, 35, 35] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280639 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 35, 35, 35, 35, 35, 35, 75, 75, 75, 35, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 35, 35, 75, 75, 75, 75, 35, 1, 1, 1] 75 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280639 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280639 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280639/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280639 Building REAL300000280640 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280640' /scratch/stefan/7769901/working/building/REAL300000280640 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280640 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280640/0 /scratch/stefan/7769901/working/building/REAL300000280640 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/880 `/scratch/stefan/7769901/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000280640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280640 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 73, 73, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37] 191 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280640 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 37, 37, 37, 37, 37, 37, 105, 105, 105, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 72, 73, 73, 37, 37, 105, 105, 105, 105, 37, 1, 1, 1] 191 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280640 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280640/1 /scratch/stefan/7769901/working/building/REAL300000280640 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/881 `/scratch/stefan/7769901/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000280640.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280640 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 71, 71, 37, 37, 37, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 37, 37, 37] 163 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280640 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 37, 37, 37, 37, 37, 37, 102, 102, 102, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 77, 77, 77, 37, 37, 102, 102, 102, 102, 37, 9, 1, 1, 1] 163 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280640 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280640 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280640/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280640/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280640 Building REAL300000280641 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280641' /scratch/stefan/7769901/working/building/REAL300000280641 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280641 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280641/0 /scratch/stefan/7769901/working/building/REAL300000280641 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/882 `/scratch/stefan/7769901/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1) `REAL300000280641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280641 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 75, 75, 75, 75, 75, 75, 75, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 75, 75] 182 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 27, 28] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280641 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [83, 75, 75, 75, 75, 75, 75, 182, 182, 182, 75, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 75, 75, 182, 182, 182, 182, 75, 1, 1] 182 rigid atoms, others: [34, 35, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280641 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280641 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280641/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280641 Building REAL300000280642 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280642' /scratch/stefan/7769901/working/building/REAL300000280642 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280642 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280642/0 /scratch/stefan/7769901/working/building/REAL300000280642 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/883 `/scratch/stefan/7769901/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000280642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280642 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 20, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 38, 38, 38] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280642 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 38, 38, 38, 38, 38, 38, 94, 94, 94, 38, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 40, 38, 38, 94, 94, 94, 94, 38, 1, 1, 1] 94 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 245 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280642 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280642 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280642/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280642 Building REAL300000280643 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280643' /scratch/stefan/7769901/working/building/REAL300000280643 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280643 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280643/0 /scratch/stefan/7769901/working/building/REAL300000280643 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/884 `/scratch/stefan/7769901/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F) `REAL300000280643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280643 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 79, 79, 79, 79, 79] 142 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280643 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 79, 79, 79, 79, 79, 79, 142, 142, 142, 79, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 79, 79, 142, 142, 142, 142, 79, 1, 1, 2, 2, 2] 142 rigid atoms, others: [37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280643 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280643 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280643/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280643 Building REAL300000280644 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280644' /scratch/stefan/7769901/working/building/REAL300000280644 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280644 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280644/0 /scratch/stefan/7769901/working/building/REAL300000280644 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/885 `/scratch/stefan/7769901/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000280644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280644 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 74, 74, 49, 74, 74, 74, 74, 74, 74, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 74, 74, 74] 157 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280644 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 74, 74, 74, 74, 74, 74, 157, 157, 157, 74, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 82, 82, 82, 74, 74, 157, 157, 157, 157, 74, 1, 1, 1] 157 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280644 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280644 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280644/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280644 Building REAL300000280645 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280645' /scratch/stefan/7769901/working/building/REAL300000280645 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280645 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280645/0 /scratch/stefan/7769901/working/building/REAL300000280645 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/886 `/scratch/stefan/7769901/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000280645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280645 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 51, 51, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37] 117 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280645 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [55, 37, 37, 37, 37, 37, 37, 103, 103, 103, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 55, 55, 55, 37, 37, 103, 103, 103, 103, 37, 1, 1, 1] 117 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280645 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280645/1 /scratch/stefan/7769901/working/building/REAL300000280645 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/887 `/scratch/stefan/7769901/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000280645.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280645 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 49, 49, 37, 37, 37, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 37, 37, 37] 108 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280645 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 37, 37, 37, 37, 37, 37, 96, 96, 96, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 51, 53, 53, 37, 37, 96, 96, 96, 96, 37, 9, 1, 1, 1] 108 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280645 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280645 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280645/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280645/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280645 Building REAL300000280646 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280646' /scratch/stefan/7769901/working/building/REAL300000280646 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280646 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280646/0 /scratch/stefan/7769901/working/building/REAL300000280646 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/888 `/scratch/stefan/7769901/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000280646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280646 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 202 conformations in input total number of sets (complete confs): 202 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 63, 63, 63, 63, 63, 63, 63, 63, 63, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 63, 63, 63, 126] 202 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280646 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 202 conformations in input total number of sets (complete confs): 202 using faster count positions algorithm for large data unique positions, atoms: [65, 63, 63, 63, 63, 63, 63, 101, 101, 101, 63, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 65, 65, 65, 63, 63, 101, 101, 101, 101, 63, 1, 1, 1, 2] 202 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280646 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280646 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280646/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280646 Building REAL300000280647 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280647' /scratch/stefan/7769901/working/building/REAL300000280647 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280647 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280647/0 /scratch/stefan/7769901/working/building/REAL300000280647 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/889 `/scratch/stefan/7769901/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280647 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 37, 51, 51, 19, 19, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 19, 19, 37, 37, 19, 19] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280647 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 19, 19, 19, 19, 19, 53, 53, 53, 19, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 27, 27, 27, 19, 19, 53, 53, 53, 53, 19, 1, 1, 2, 2, 1, 1] 115 rigid atoms, others: [36, 37, 40, 41, 13, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280647 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280647/1 /scratch/stefan/7769901/working/building/REAL300000280647 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/890 `/scratch/stefan/7769901/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280647.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280647 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 33, 37, 37, 19, 19, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 19, 19, 33, 33, 19, 19] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280647 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 19, 19, 19, 19, 19, 19, 45, 45, 45, 19, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 23, 23, 23, 19, 19, 45, 45, 45, 45, 19, 5, 1, 1, 2, 2, 1, 1] 63 rigid atoms, others: [37, 38, 41, 42, 13, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280647 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280647 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280647/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280647/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280647 Building REAL300000280648 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280648' /scratch/stefan/7769901/working/building/REAL300000280648 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280648 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280648/0 /scratch/stefan/7769901/working/building/REAL300000280648 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/891 `/scratch/stefan/7769901/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300000280648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280648 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 25, 25, 25, 60, 60, 60, 60, 60, 60, 60, 60, 60, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 60, 60, 60, 60, 60, 60] 111 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 150 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280648 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [64, 60, 60, 60, 60, 60, 60, 111, 111, 111, 60, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 60, 60, 111, 111, 111, 111, 60, 1, 1, 1, 2, 2, 2] 111 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 275 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280648 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280648/1 /scratch/stefan/7769901/working/building/REAL300000280648 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/892 `/scratch/stefan/7769901/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300000280648.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280648 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 10, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 10, 49, 49, 49, 49, 49, 49] 90 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280648 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 49, 49, 49, 49, 49, 49, 90, 90, 90, 49, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 57, 57, 57, 49, 49, 90, 90, 90, 90, 49, 13, 1, 1, 1, 2, 2, 2] 90 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280648 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280648 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280648/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280648/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280648 Building REAL300000280649 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280649' /scratch/stefan/7769901/working/building/REAL300000280649 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280649 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280649/0 /scratch/stefan/7769901/working/building/REAL300000280649 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/893 `/scratch/stefan/7769901/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1) `REAL300000280649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280649 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 69, 69, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37] 134 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280649 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 37, 37, 37, 37, 37, 37, 85, 85, 85, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 37, 37, 85, 85, 85, 85, 37, 1, 2, 2, 2, 1] 134 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280649 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280649/1 /scratch/stefan/7769901/working/building/REAL300000280649 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/894 `/scratch/stefan/7769901/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1) `REAL300000280649.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280649 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 65, 65, 35, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 35, 35, 35, 35, 35] 117 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280649 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [65, 35, 35, 35, 35, 35, 35, 73, 73, 73, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 65, 65, 65, 35, 35, 73, 73, 73, 73, 35, 9, 1, 2, 2, 2, 1] 117 rigid atoms, others: [38, 42, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280649 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280649 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280649/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280649/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280649 Building REAL300000280650 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280650' /scratch/stefan/7769901/working/building/REAL300000280650 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280650 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280650/0 /scratch/stefan/7769901/working/building/REAL300000280650 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/895 `/scratch/stefan/7769901/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000280650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280650 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 51, 51, 37, 45, 51, 51, 51, 51, 51, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 51, 51, 51, 51, 51, 51] 100 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280650 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [53, 51, 51, 51, 51, 51, 51, 100, 100, 100, 51, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 51, 51, 100, 100, 100, 100, 51, 1, 1, 1, 2, 2, 2] 100 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280650 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280650/1 /scratch/stefan/7769901/working/building/REAL300000280650 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/896 `/scratch/stefan/7769901/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000280650.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280650 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 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] 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 25, 25, 25, 31, 31, 30, 31, 31, 31, 31, 31, 31, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 10, 31, 31, 31, 31, 31, 31] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280650 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 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] 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: [37, 31, 31, 31, 31, 31, 31, 63, 63, 63, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 31, 31, 63, 63, 63, 63, 31, 9, 1, 1, 1, 2, 2, 2] 63 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280650 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280650 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280650/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280650/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280650 Building REAL300000280651 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280651' /scratch/stefan/7769901/working/building/REAL300000280651 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280651 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280651/0 /scratch/stefan/7769901/working/building/REAL300000280651 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/897 `/scratch/stefan/7769901/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1) `REAL300000280651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280651 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37, 37, 37, 37] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280651 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 37, 37, 37, 75, 75, 75, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 37, 75, 75, 75, 75, 37, 1, 2, 2, 2, 2, 2, 2, 1] 75 rigid atoms, others: [37, 44, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280651 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280651/1 /scratch/stefan/7769901/working/building/REAL300000280651 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/898 `/scratch/stefan/7769901/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1) `REAL300000280651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280651 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 7, 33, 33, 33, 33, 33, 33, 33, 33] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280651 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 33, 33, 33, 33, 33, 33, 61, 61, 61, 33, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 33, 33, 61, 61, 61, 61, 33, 9, 1, 2, 2, 2, 2, 2, 2, 1] 61 rigid atoms, others: [38, 13, 45, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280651 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280651 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280651/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280651/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280651 Building REAL300000280652 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280652' /scratch/stefan/7769901/working/building/REAL300000280652 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280652 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280652/0 /scratch/stefan/7769901/working/building/REAL300000280652 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/899 `/scratch/stefan/7769901/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C) `REAL300000280652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280652 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 24, 24, 24, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 57, 57, 57, 57, 57, 57, 57, 57] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280652 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 57, 57, 57, 57, 57, 57, 107, 107, 107, 57, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 63, 63, 57, 57, 107, 107, 107, 107, 57, 1, 1, 2, 2, 2, 2, 2, 2] 107 rigid atoms, others: [37, 38, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280652 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280652/1 /scratch/stefan/7769901/working/building/REAL300000280652 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/900 `/scratch/stefan/7769901/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C) `REAL300000280652.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280652 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 10, 26, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 10, 47, 47, 47, 47, 47, 47, 47, 47] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280652 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C)C(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [55, 47, 47, 47, 47, 47, 47, 87, 87, 87, 47, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 55, 55, 55, 47, 47, 87, 87, 87, 87, 47, 13, 1, 1, 2, 2, 2, 2, 2, 2] 87 rigid atoms, others: [38, 39, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280652 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280652 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280652/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280652/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280652 Building REAL300000280653 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280653' /scratch/stefan/7769901/working/building/REAL300000280653 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280653 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280653/0 /scratch/stefan/7769901/working/building/REAL300000280653 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/901 `/scratch/stefan/7769901/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F) `REAL300000280653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280653 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 79, 79, 79, 112, 112, 79, 79, 79, 79, 79, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 79, 79, 79, 79, 79] 190 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280653 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 79, 79, 79, 79, 79, 79, 144, 144, 144, 79, 25, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 111, 111, 111, 79, 79, 144, 144, 144, 144, 79, 1, 2, 2, 2, 1] 190 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280653 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280653 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280653/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280653 Building REAL300000280654 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280654' /scratch/stefan/7769901/working/building/REAL300000280654 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280654 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280654/0 /scratch/stefan/7769901/working/building/REAL300000280654 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/902 `/scratch/stefan/7769901/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F) `REAL300000280654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280654 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 80, 80, 80, 80, 80, 80, 125, 125, 80, 80, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 80, 80, 80, 80, 80] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280654 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 80, 80, 80, 80, 80, 149, 149, 149, 80, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 116, 116, 116, 80, 80, 149, 149, 149, 149, 80, 1, 2, 2, 2, 1] 201 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280654 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280654 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280654/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280654 Building REAL300000280655 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280655' /scratch/stefan/7769901/working/building/REAL300000280655 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280655 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280655/0 /scratch/stefan/7769901/working/building/REAL300000280655 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/903 `/scratch/stefan/7769901/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-]) `REAL300000280655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280655 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 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, 3, 3, 7, 7, 7, 7, 4, 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] 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 37, 37, 37, 74, 74, 74, 37, 37, 37, 37, 43, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 37, 74, 74, 74, 74, 37, 37, 43, 43, 43, 1] 157 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 44, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280655 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 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, 3, 3, 7, 7, 7, 7, 4, 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] 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: [81, 37, 37, 37, 37, 19, 7, 19, 19, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 37, 37, 37, 39, 39, 81, 81, 81, 81, 81, 37, 37, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 37] 157 rigid atoms, others: [34, 39, 40, 9, 10, 11, 12, 13, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280655 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280655/1 /scratch/stefan/7769901/working/building/REAL300000280655 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/904 `/scratch/stefan/7769901/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-]) `REAL300000280655.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280655 none CCC1=CC=C(S(=O)(=O)NC2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 4, 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] 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 57, 57, 57, 33, 33, 33, 33, 39, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 9, 33, 57, 57, 57, 57, 33, 33, 39, 39, 39, 1] 123 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 45, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280655 none CCC1=CC=C(S(=O)(=O)NC2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 4, 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] 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: [76, 33, 33, 33, 33, 19, 7, 19, 19, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 33, 33, 33, 41, 41, 76, 76, 76, 76, 76, 33, 33, 7, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 33] 123 rigid atoms, others: [35, 40, 9, 10, 11, 12, 13, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280655 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280655 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280655/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280655/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280655 Building REAL300000280656 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280656' /scratch/stefan/7769901/working/building/REAL300000280656 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280656 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280656/0 /scratch/stefan/7769901/working/building/REAL300000280656 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/905 `/scratch/stefan/7769901/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-]) `REAL300000280656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280656 none CCN1C=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 39, 39, 39, 90, 90, 90, 39, 39, 39, 39, 61, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 39, 90, 90, 90, 90, 39, 39, 61, 61, 61, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 42, 21, 22, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 276 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280656 none CCN1C=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 39, 39, 39, 21, 7, 21, 21, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 39, 39, 39, 39, 39, 96, 96, 96, 96, 96, 39, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 39] 201 rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 403 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280656 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280656 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280656/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280656 Building REAL300000280657 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280657' /scratch/stefan/7769901/working/building/REAL300000280657 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280657 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280657/0 /scratch/stefan/7769901/working/building/REAL300000280657 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/906 `/scratch/stefan/7769901/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1) `REAL300000280657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280657 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 73, 73, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37, 37] 183 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280657 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 37, 37, 37, 37, 37, 37, 105, 105, 105, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 73, 73, 73, 37, 37, 105, 105, 105, 105, 37, 1, 1, 2, 2, 2, 1] 183 rigid atoms, others: [36, 37, 41, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280657 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280657/1 /scratch/stefan/7769901/working/building/REAL300000280657 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/907 `/scratch/stefan/7769901/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1) `REAL300000280657.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280657 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 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] 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, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 73, 73, 37, 37, 37, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 7, 37, 37, 37, 37, 37, 37] 176 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280657 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 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] 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: [82, 37, 37, 37, 37, 37, 37, 105, 105, 105, 37, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 82, 82, 82, 37, 37, 105, 105, 105, 105, 37, 9, 1, 1, 2, 2, 2, 1] 176 rigid atoms, others: [37, 38, 42, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280657 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280657 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280657/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280657/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280657 Building REAL300000280658 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280658' /scratch/stefan/7769901/working/building/REAL300000280658 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280658 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280658/0 /scratch/stefan/7769901/working/building/REAL300000280658 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/908 `/scratch/stefan/7769901/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C) `REAL300000280658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280658 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 41, 41, 41, 69, 69, 41, 41, 41, 41, 41, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 41, 41, 41, 41, 41] 105 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280658 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [67, 41, 41, 41, 41, 41, 41, 67, 67, 67, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 67, 67, 67, 41, 41, 67, 67, 67, 67, 41, 1, 1, 2, 2, 2] 105 rigid atoms, others: [37, 38, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 228 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280658 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280658/1 /scratch/stefan/7769901/working/building/REAL300000280658 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/909 `/scratch/stefan/7769901/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C) `REAL300000280658.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280658 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 23, 23, 23, 46, 46, 46, 82, 82, 46, 46, 46, 46, 46, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 8, 46, 46, 46, 46, 46] 129 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280658 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [86, 46, 46, 46, 46, 46, 46, 79, 79, 79, 46, 12, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 86, 86, 86, 46, 46, 79, 79, 79, 79, 46, 12, 1, 1, 2, 2, 2] 129 rigid atoms, others: [38, 39, 13, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280658 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280658 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280658/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280658/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280658 Building REAL300000280659 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280659' /scratch/stefan/7769901/working/building/REAL300000280659 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280659 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280659/0 /scratch/stefan/7769901/working/building/REAL300000280659 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/910 `/scratch/stefan/7769901/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000280659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280659 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 82, 82, 82, 82, 82, 124, 124, 82, 82, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 82, 82, 82] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280659 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 82, 82, 82, 82, 82, 141, 141, 141, 82, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 124, 124, 124, 82, 82, 141, 141, 141, 141, 82, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 13, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280659 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280659 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280659/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280659 Building REAL300000280660 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280660' /scratch/stefan/7769901/working/building/REAL300000280660 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280660 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280660/0 /scratch/stefan/7769901/working/building/REAL300000280660 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/911 `/scratch/stefan/7769901/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1) `REAL300000280660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280660 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 37, 37, 37, 37, 37] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280660 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 87, 87, 87, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 37, 87, 87, 87, 87, 37, 1, 2, 2, 2, 1] 87 rigid atoms, others: [37, 41, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280660 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280660/1 /scratch/stefan/7769901/working/building/REAL300000280660 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/912 `/scratch/stefan/7769901/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1) `REAL300000280660.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280660 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 19, 19, 19, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 7, 36, 36, 36, 36, 36] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280660 none COC1=CC=C(NC(C)=O)C=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 36, 36, 36, 36, 36, 36, 70, 70, 70, 36, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 36, 36, 70, 70, 70, 70, 36, 9, 1, 2, 2, 2, 1] 70 rigid atoms, others: [38, 42, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280660 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280660 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280660/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280660/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280660 Building REAL300000280661 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280661' /scratch/stefan/7769901/working/building/REAL300000280661 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280661 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280661/0 /scratch/stefan/7769901/working/building/REAL300000280661 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/913 `/scratch/stefan/7769901/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300000280661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280661 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 95, 95, 95, 95, 95, 95, 95, 95, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 95, 95, 95] 173 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280661 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [107, 95, 95, 95, 95, 95, 95, 173, 173, 173, 95, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 107, 107, 107, 95, 95, 173, 173, 173, 173, 95, 1, 1, 1] 173 rigid atoms, others: [35, 36, 37, 13, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280661 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280661 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280661/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280661 Building REAL300000280662 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280662' /scratch/stefan/7769901/working/building/REAL300000280662 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280662 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280662/0 /scratch/stefan/7769901/working/building/REAL300000280662 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/914 `/scratch/stefan/7769901/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC) `REAL300000280662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280662 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 21, 21, 21, 78, 78, 41, 78, 78, 78, 78, 78, 78, 109, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 78, 78, 78, 109, 109, 109] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 36, 30, 31] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280662 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 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: [106, 78, 78, 78, 78, 78, 78, 163, 163, 163, 78, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 106, 106, 106, 78, 78, 163, 163, 163, 163, 78, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [37, 38, 39, 13, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280662 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280662 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280662/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280662 Building REAL300000280663 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280663' /scratch/stefan/7769901/working/building/REAL300000280663 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280663 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280663/0 /scratch/stefan/7769901/working/building/REAL300000280663 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/915 `/scratch/stefan/7769901/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000280663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280663 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 23, 23, 69, 69, 69, 69, 69, 69, 69, 69, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 69] 151 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280663 none COC1=CC=C(NC(C)=O)C=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [75, 69, 69, 69, 69, 69, 69, 151, 151, 151, 69, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 75, 69, 69, 151, 151, 151, 151, 69, 1] 151 rigid atoms, others: [35, 13, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280663 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280663 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280663/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280663 Building REAL300000280664 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280664' /scratch/stefan/7769901/working/building/REAL300000280664 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280664 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280664/0 /scratch/stefan/7769901/working/building/REAL300000280664 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/916 `/scratch/stefan/7769901/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C(C(=O)[O-])O1) `REAL300000280664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280664 none CCC1=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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] 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: [6, 1, 1, 1, 1, 7, 7, 7, 21, 39, 39, 39, 72, 72, 72, 39, 39, 39, 39, 52, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 39, 72, 72, 72, 72, 39, 39, 52, 52, 52, 1] 77 rigid atoms, others: [1, 2, 3, 4, 41, 20, 21, 22, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280664 none CCC1=C(S(=O)(=O)[N-]C2=CC(NC(C)=O)=CC=C2OC)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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] 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: [46, 39, 39, 11, 5, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 39, 39, 39, 39, 39, 39, 46, 46, 46, 46, 46, 1, 4, 4, 4, 4, 1, 1, 3, 3, 3, 39] 77 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280664 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280664 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280664/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280664 Building REAL300000280665 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280665' /scratch/stefan/7769901/working/building/REAL300000280665 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280665 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280665/0 /scratch/stefan/7769901/working/building/REAL300000280665 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/917 `/scratch/stefan/7769901/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F) `REAL300000280665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280665 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 55, 55, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280665 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 23, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280665 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280665/1 /scratch/stefan/7769901/working/building/REAL300000280665 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/918 `/scratch/stefan/7769901/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F) `REAL300000280665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280665 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 38, 23, 24, 25, 26, 27, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280665 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51] 51 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280665 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280665 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280665/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280665/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280665 Building REAL300000280666 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280666' /scratch/stefan/7769901/working/building/REAL300000280666 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280666 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280666/0 /scratch/stefan/7769901/working/building/REAL300000280666 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/919 `/scratch/stefan/7769901/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280666 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 2, 2, 2, 5, 13, 13, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280666 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 13 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280666 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280666 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280666/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280666 Building REAL300000280667 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280667' /scratch/stefan/7769901/working/building/REAL300000280667 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280667 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280667/0 /scratch/stefan/7769901/working/building/REAL300000280667 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/920 `/scratch/stefan/7769901/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280667 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 25, 25, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280667 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 25, 26, 27, 28, 29]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280667 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280667/1 /scratch/stefan/7769901/working/building/REAL300000280667 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/921 `/scratch/stefan/7769901/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280667.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280667 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280667 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23] 23 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280667 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280667 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280667/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280667/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280667 Building REAL300000280668 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280668' /scratch/stefan/7769901/working/building/REAL300000280668 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280668 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280668/0 /scratch/stefan/7769901/working/building/REAL300000280668 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/922 `/scratch/stefan/7769901/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280668 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 25, 93, 93, 63, 93, 93, 93, 93, 93, 93, 93, 93, 93, 3, 3, 3, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93] 93 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280668 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 28, 29, 30, 31]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280668 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280668/1 /scratch/stefan/7769901/working/building/REAL300000280668 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/923 `/scratch/stefan/7769901/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280668.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280668 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 4, 4, 4, 1, 1, 1, 25, 76, 76, 76, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 31] set([0, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280668 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 31, 11, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280668 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280668 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280668/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280668/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280668 Building REAL300000280669 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280669' /scratch/stefan/7769901/working/building/REAL300000280669 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280669 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280669/0 /scratch/stefan/7769901/working/building/REAL300000280669 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/924 `/scratch/stefan/7769901/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280669 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 51, 51, 17, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 3, 3, 1, 1, 9, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1] 51 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 43, 26, 27, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280669 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 9, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51] 51 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 43, 42, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 139 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280669 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280669/1 /scratch/stefan/7769901/working/building/REAL300000280669 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/925 `/scratch/stefan/7769901/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280669.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280669 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 52, 52, 9, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 3, 3, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1] 52 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 41, 26, 27, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280669 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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, 27, 9, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52] 52 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 42, 41, 26, 27, 28, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280669 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280669 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280669/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280669/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280669 Building REAL300000280670 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280670' /scratch/stefan/7769901/working/building/REAL300000280670 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280670 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280670/0 /scratch/stefan/7769901/working/building/REAL300000280670 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/926 `/scratch/stefan/7769901/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280670 none CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 49, 49, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280670 none CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 6, 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] 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, 27, 11, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 49 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 42, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280670 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280670 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280670/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280670 Building REAL300000280671 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280671' /scratch/stefan/7769901/working/building/REAL300000280671 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280671 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280671/0 /scratch/stefan/7769901/working/building/REAL300000280671 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/927 `/scratch/stefan/7769901/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280671 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 32, 32, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 38, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280671 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 24, 8, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 32 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 26, 27, 28]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280671 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280671/1 /scratch/stefan/7769901/working/building/REAL300000280671 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/928 `/scratch/stefan/7769901/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280671.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280671 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280671 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 30 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280671 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280671 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280671/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280671/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280671 Building REAL300000280672 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280672' /scratch/stefan/7769901/working/building/REAL300000280672 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280672 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280672/0 /scratch/stefan/7769901/working/building/REAL300000280672 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/929 `/scratch/stefan/7769901/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl) `REAL300000280672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280672 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 35, 35, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280672 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 23, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280672 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280672/1 /scratch/stefan/7769901/working/building/REAL300000280672 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/930 `/scratch/stefan/7769901/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl) `REAL300000280672.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280672 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 38, 23, 24, 25, 26, 27, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280672 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280672 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280672 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280672/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280672/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280672 Building REAL300000280673 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280673' /scratch/stefan/7769901/working/building/REAL300000280673 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280673 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280673/0 /scratch/stefan/7769901/working/building/REAL300000280673 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/931 `/scratch/stefan/7769901/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C) `REAL300000280673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280673 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280673 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280673 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280673/1 /scratch/stefan/7769901/working/building/REAL300000280673 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/932 `/scratch/stefan/7769901/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C) `REAL300000280673.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280673 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 2, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280673 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 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, 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, 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, 19, 10, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23] 23 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280673 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280673 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280673/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280673/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280673 Building REAL300000280674 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280674' /scratch/stefan/7769901/working/building/REAL300000280674 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280674 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280674/0 /scratch/stefan/7769901/working/building/REAL300000280674 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/933 `/scratch/stefan/7769901/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280674 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 55, 55, 44, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 38, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280674 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 33, 12, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 55 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 26, 27, 28]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280674 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280674 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280674/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280674 Building REAL300000280675 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280675' /scratch/stefan/7769901/working/building/REAL300000280675 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280675 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280675/0 /scratch/stefan/7769901/working/building/REAL300000280675 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/934 `/scratch/stefan/7769901/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280675 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 13, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 39, 39, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 7, 7, 3, 3, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 93 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 44, 45, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280675 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 61, 21, 21, 39, 39, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 93, 93, 61, 61, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 93 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280675 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280675/1 /scratch/stefan/7769901/working/building/REAL300000280675 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/935 `/scratch/stefan/7769901/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280675.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280675 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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: [2, 7, 2, 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, 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: [9, 3, 9, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 42, 42, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 3, 3, 3, 3, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1] 56 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 43, 44, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280675 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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: [2, 7, 2, 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, 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, 23, 42, 42, 42, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 56, 56, 56, 56, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 56 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280675 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280675 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280675/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280675/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280675 Building REAL300000280676 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280676' /scratch/stefan/7769901/working/building/REAL300000280676 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280676 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280676/0 /scratch/stefan/7769901/working/building/REAL300000280676 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/936 `/scratch/stefan/7769901/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280676 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 51, 51, 36, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280676 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 12, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51] 51 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280676 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280676 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280676/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280676 Building REAL300000280677 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280677' /scratch/stefan/7769901/working/building/REAL300000280677 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280677 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280677/0 /scratch/stefan/7769901/working/building/REAL300000280677 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/937 `/scratch/stefan/7769901/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280677 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 8, 9, 10, 30, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280677 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280677 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280677/1 /scratch/stefan/7769901/working/building/REAL300000280677 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/938 `/scratch/stefan/7769901/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280677.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280677 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 8, 9, 10, 30, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280677 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 25, 10, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280677 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280677 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280677/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280677/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280677 Building REAL300000280678 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280678' /scratch/stefan/7769901/working/building/REAL300000280678 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280678 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280678/0 /scratch/stefan/7769901/working/building/REAL300000280678 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/939 `/scratch/stefan/7769901/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280678 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 19, 30, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 46, 46, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 19, 19, 1, 1, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 169 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 43, 26, 27, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 232 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280678 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 46, 25, 46, 46, 25, 7, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 169, 169, 46, 46, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 169 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 43, 42, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 712 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280678 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280678 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280678/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280678 Building REAL300000280679 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280679' /scratch/stefan/7769901/working/building/REAL300000280679 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280679 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280679/0 /scratch/stefan/7769901/working/building/REAL300000280679 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/940 `/scratch/stefan/7769901/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280679 none CN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 3, 3, 3, 9, 31, 31, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 2, 2, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 40, 21, 22, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280679 none CN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 31 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 40, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280679 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280679/1 /scratch/stefan/7769901/working/building/REAL300000280679 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/941 `/scratch/stefan/7769901/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280679.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280679 none CN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 33, 33, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 39, 21, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280679 none CN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280679 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280679 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280679/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280679/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280679 Building REAL300000280680 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280680' /scratch/stefan/7769901/working/building/REAL300000280680 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280680 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280680/0 /scratch/stefan/7769901/working/building/REAL300000280680 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/942 `/scratch/stefan/7769901/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280680 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 2, 2, 1, 1, 1, 5, 5, 5, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 2, 1, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280680 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 9, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 64, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 64 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280680 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280680 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280680/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280680 Building REAL300000280681 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280681' /scratch/stefan/7769901/working/building/REAL300000280681 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280681 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280681/0 /scratch/stefan/7769901/working/building/REAL300000280681 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/943 `/scratch/stefan/7769901/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280681 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 17, 80, 80, 36, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 2, 2, 2, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1] 80 rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280681 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 31, 11, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 25, 26, 27, 28]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280681 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280681 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280681/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280681 Building REAL300000280682 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280682' /scratch/stefan/7769901/working/building/REAL300000280682 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280682 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280682/0 /scratch/stefan/7769901/working/building/REAL300000280682 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/944 `/scratch/stefan/7769901/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280682 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 3, 3, 3, 5, 33, 33, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 2, 2, 2, 1, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280682 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280682 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280682 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280682/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280682 Building REAL300000280683 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280683' /scratch/stefan/7769901/working/building/REAL300000280683 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280683 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280683/0 /scratch/stefan/7769901/working/building/REAL300000280683 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/945 `/scratch/stefan/7769901/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1) `REAL300000280683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280683 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 35, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280683 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280683 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280683/1 /scratch/stefan/7769901/working/building/REAL300000280683 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/946 `/scratch/stefan/7769901/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1) `REAL300000280683.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280683 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 36] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280683 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280683 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280683 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280683/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280683/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280683 Building REAL300000280684 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280684' /scratch/stefan/7769901/working/building/REAL300000280684 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280684 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280684/0 /scratch/stefan/7769901/working/building/REAL300000280684 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/947 `/scratch/stefan/7769901/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280684 none COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 53, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 97 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 43, 23, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280684 none COC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 53, 53, 53, 53, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 97, 97, 97, 97, 97, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 97 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280684 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280684 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280684/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280684 Building REAL300000280685 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280685' /scratch/stefan/7769901/working/building/REAL300000280685 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280685 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280685/0 /scratch/stefan/7769901/working/building/REAL300000280685 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/948 `/scratch/stefan/7769901/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280685 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 57, 57, 27, 57, 57, 57, 57, 57, 57, 57, 57, 57, 6, 6, 6, 6, 6, 1, 1, 1, 13, 57, 57, 57, 57, 57, 57, 57, 57, 57] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 11, 35] set([0, 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]) total number of confs: 172 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280685 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 57, 57, 57, 57, 57, 57, 57, 57, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280685 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280685/1 /scratch/stefan/7769901/working/building/REAL300000280685 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/949 `/scratch/stefan/7769901/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280685.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280685 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 57, 57, 31, 57, 57, 57, 57, 57, 57, 57, 57, 57, 5, 5, 5, 5, 5, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 11, 35] set([0, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280685 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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, 57, 57, 57, 57, 57, 57, 57, 57, 57, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280685 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280685 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280685/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280685/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280685 Building REAL300000280686 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280686' /scratch/stefan/7769901/working/building/REAL300000280686 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280686 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280686/0 /scratch/stefan/7769901/working/building/REAL300000280686 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/950 `/scratch/stefan/7769901/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1) `REAL300000280686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280686 none CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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] 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, 7, 7, 7, 15, 37, 37, 29, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 38, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280686 none CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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] 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, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280686 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280686/1 /scratch/stefan/7769901/working/building/REAL300000280686 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/951 `/scratch/stefan/7769901/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1) `REAL300000280686.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280686 none CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 5, 5, 5, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 32 rigid atoms, others: [0, 1, 2, 3, 39, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280686 none CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280686 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280686 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280686/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280686/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280686 Building REAL300000280687 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280687' /scratch/stefan/7769901/working/building/REAL300000280687 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280687 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280687/0 /scratch/stefan/7769901/working/building/REAL300000280687 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/952 `/scratch/stefan/7769901/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280687 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 22, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 2, 2, 2, 1, 2, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1] 162 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 42, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280687 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [81, 81, 81, 81, 81, 81, 81, 81, 81, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 162, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81] 162 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 42, 32, 27, 28, 29, 30, 31]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280687 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280687/1 /scratch/stefan/7769901/working/building/REAL300000280687 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/953 `/scratch/stefan/7769901/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280687.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280687 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 41, 41, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 1, 2, 12, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 82 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 43, 27, 31] set([5, 6, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280687 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 11, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 82, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 82 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 43, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280687 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280687 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280687/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280687/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280687 Building REAL300000280688 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280688' /scratch/stefan/7769901/working/building/REAL300000280688 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280688 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280688/0 /scratch/stefan/7769901/working/building/REAL300000280688 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/954 `/scratch/stefan/7769901/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280688 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 4, 4, 4, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280688 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 9, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280688 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280688/1 /scratch/stefan/7769901/working/building/REAL300000280688 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/955 `/scratch/stefan/7769901/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280688.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280688 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280688 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 10, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280688 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280688 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280688/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280688/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280688 Building REAL300000280689 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280689' /scratch/stefan/7769901/working/building/REAL300000280689 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280689 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280689/0 /scratch/stefan/7769901/working/building/REAL300000280689 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/956 `/scratch/stefan/7769901/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1) `REAL300000280689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280689 none CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 5, 5, 5, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 1, 2, 2, 2, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 39, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280689 none CC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280689 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280689/1 /scratch/stefan/7769901/working/building/REAL300000280689 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/957 `/scratch/stefan/7769901/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1) `REAL300000280689.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280689 none CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 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, 5, 5, 5, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 38, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280689 none CC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 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, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 29 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280689 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280689 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280689/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280689/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280689 Building REAL300000280690 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280690' /scratch/stefan/7769901/working/building/REAL300000280690 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280690 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280690/0 /scratch/stefan/7769901/working/building/REAL300000280690 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/958 `/scratch/stefan/7769901/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1) `REAL300000280690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280690 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 28] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280690 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 9, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 24, 25, 26, 27, 28]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280690 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280690/1 /scratch/stefan/7769901/working/building/REAL300000280690 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/959 `/scratch/stefan/7769901/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1) `REAL300000280690.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280690 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 24, 25, 26, 27, 28] set([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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280690 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 21, 21, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280690 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280690 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280690/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280690/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280690 Building REAL300000280691 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280691' /scratch/stefan/7769901/working/building/REAL300000280691 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280691 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280691/0 /scratch/stefan/7769901/working/building/REAL300000280691 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/960 `/scratch/stefan/7769901/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F) `REAL300000280691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280691 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 57, 57, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280691 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280691 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280691/1 /scratch/stefan/7769901/working/building/REAL300000280691 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/961 `/scratch/stefan/7769901/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F) `REAL300000280691.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280691 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280691 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 24, 25, 26, 27, 28]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280691 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280691 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280691/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280691/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280691 Building REAL300000280692 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280692' /scratch/stefan/7769901/working/building/REAL300000280692 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280692 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280692/0 /scratch/stefan/7769901/working/building/REAL300000280692 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/962 `/scratch/stefan/7769901/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)S1) `REAL300000280692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280692 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 17, 43, 43, 35, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 43 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280692 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 11, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280692 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280692 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280692/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280692 Building REAL300000280693 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280693' /scratch/stefan/7769901/working/building/REAL300000280693 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280693 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280693/0 /scratch/stefan/7769901/working/building/REAL300000280693 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/963 `/scratch/stefan/7769901/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280693 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280693 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280693 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280693/1 /scratch/stefan/7769901/working/building/REAL300000280693 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/964 `/scratch/stefan/7769901/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280693.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280693 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280693 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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, 15, 9, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 22 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 26, 27, 28]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280693 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280693 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280693/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280693/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280693 Building REAL300000280694 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280694' /scratch/stefan/7769901/working/building/REAL300000280694 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280694 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280694/0 /scratch/stefan/7769901/working/building/REAL300000280694 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/965 `/scratch/stefan/7769901/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F) `REAL300000280694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280694 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 25, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 2, 2, 2, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 32, 26, 27, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280694 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 12, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280694 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280694 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280694/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280694 Building REAL300000280695 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280695' /scratch/stefan/7769901/working/building/REAL300000280695 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280695 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280695/0 /scratch/stefan/7769901/working/building/REAL300000280695 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/966 `/scratch/stefan/7769901/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1) `REAL300000280695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280695 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 28] set([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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280695 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 24, 25, 26, 27, 28]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280695 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280695/1 /scratch/stefan/7769901/working/building/REAL300000280695 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/967 `/scratch/stefan/7769901/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1) `REAL300000280695.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280695 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 24, 25, 26, 27, 28] set([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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280695 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 37 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280695 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280695 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280695/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280695/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280695 Building REAL300000280696 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280696' /scratch/stefan/7769901/working/building/REAL300000280696 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280696 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280696/0 /scratch/stefan/7769901/working/building/REAL300000280696 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/968 `/scratch/stefan/7769901/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl) `REAL300000280696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280696 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 41, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280696 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280696 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280696/1 /scratch/stefan/7769901/working/building/REAL300000280696 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/969 `/scratch/stefan/7769901/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl) `REAL300000280696.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280696 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280696 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 24, 25, 26, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280696 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280696 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280696/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280696/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280696 Building REAL300000280697 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280697' /scratch/stefan/7769901/working/building/REAL300000280697 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280697 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280697/0 /scratch/stefan/7769901/working/building/REAL300000280697 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/970 `/scratch/stefan/7769901/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280697 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 1, 1, 1, 1, 7, 7, 7, 23, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 2, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280697 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 31, 12, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 112, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56] 112 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280697 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280697/1 /scratch/stefan/7769901/working/building/REAL300000280697 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/971 `/scratch/stefan/7769901/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280697.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280697 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280697 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280697 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280697 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280697/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280697/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280697 Building REAL300000280698 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280698' /scratch/stefan/7769901/working/building/REAL300000280698 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280698 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280698/0 /scratch/stefan/7769901/working/building/REAL300000280698 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/972 `/scratch/stefan/7769901/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280698 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 25, 26, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280698 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 9, 3, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 17 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 42, 41, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280698 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280698/1 /scratch/stefan/7769901/working/building/REAL300000280698 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/973 `/scratch/stefan/7769901/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1) `REAL300000280698.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280698 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 1, 2, 9, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280698 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 23, 23, 23, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 25, 26, 27, 28, 29, 30]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280698 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280698 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280698/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280698/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280698 Building REAL300000280699 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280699' /scratch/stefan/7769901/working/building/REAL300000280699 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280699 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280699/0 /scratch/stefan/7769901/working/building/REAL300000280699 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/974 `/scratch/stefan/7769901/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280699 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280699 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280699 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280699/1 /scratch/stefan/7769901/working/building/REAL300000280699 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/975 `/scratch/stefan/7769901/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280699.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280699 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280699 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 27, 28, 29, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280699 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280699 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280699/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280699/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280699 Building REAL300000280700 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280700' /scratch/stefan/7769901/working/building/REAL300000280700 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280700 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280700/0 /scratch/stefan/7769901/working/building/REAL300000280700 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/976 `/scratch/stefan/7769901/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F) `REAL300000280700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280700 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 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, 3, 3, 3, 9, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 42, 21, 22, 23, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280700 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 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, 28, 11, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54] 54 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280700 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280700/1 /scratch/stefan/7769901/working/building/REAL300000280700 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/977 `/scratch/stefan/7769901/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F) `REAL300000280700.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280700 none CC1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 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, 3, 3, 3, 9, 50, 50, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 41, 21, 22, 23, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280700 none CC1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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 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, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280700 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280700 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280700/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280700/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280700 Building REAL300000280701 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280701' /scratch/stefan/7769901/working/building/REAL300000280701 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280701 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280701/0 /scratch/stefan/7769901/working/building/REAL300000280701 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/978 `/scratch/stefan/7769901/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280701 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280701 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280701 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280701 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280701/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280701 Building REAL300000280702 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280702' /scratch/stefan/7769901/working/building/REAL300000280702 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280702 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280702/0 /scratch/stefan/7769901/working/building/REAL300000280702 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/979 `/scratch/stefan/7769901/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1C) `REAL300000280702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280702 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 4, 42, 21, 22, 23, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280702 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280702 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280702 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280702/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280702 Building REAL300000280703 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280703' /scratch/stefan/7769901/working/building/REAL300000280703 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280703 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280703/0 /scratch/stefan/7769901/working/building/REAL300000280703 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/980 `/scratch/stefan/7769901/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(C)=C1C(=O)[O-]) `REAL300000280703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280703 none CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 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, 6, 6, 4, 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] 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, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 22, 23, 24, 25, 31] set([6, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280703 none CC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 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, 6, 6, 4, 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] 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, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25] 25 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280703 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280703 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280703/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280703 Building REAL300000280704 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280704' /scratch/stefan/7769901/working/building/REAL300000280704 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280704 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280704/0 /scratch/stefan/7769901/working/building/REAL300000280704 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/981 `/scratch/stefan/7769901/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280704 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 94, 94, 48, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 3, 3, 2, 2, 2, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280704 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94] 94 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280704 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280704/1 /scratch/stefan/7769901/working/building/REAL300000280704 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/982 `/scratch/stefan/7769901/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280704.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280704 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 95, 95, 45, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 3, 3, 2, 2, 2, 1, 23, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280704 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 95, 95, 95, 95, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95] 95 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280704 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280704 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280704/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280704/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280704 Building REAL300000280705 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280705' /scratch/stefan/7769901/working/building/REAL300000280705 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280705 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280705/0 /scratch/stefan/7769901/working/building/REAL300000280705 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/983 `/scratch/stefan/7769901/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280705 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 1, 7, 7, 7, 25, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 2, 2, 2, 1, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1] 103 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 41, 27, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280705 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 103, 103, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103] 103 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 41, 27, 28, 29, 30, 31]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280705 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280705 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280705/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280705 Building REAL300000280706 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280706' /scratch/stefan/7769901/working/building/REAL300000280706 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280706 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280706/0 /scratch/stefan/7769901/working/building/REAL300000280706 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/984 `/scratch/stefan/7769901/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280706 none CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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: [4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 45, 23, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280706 none CCC1=CC=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 29, 29, 29, 29, 21, 11, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 44, 44, 58, 58, 58, 58, 58, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29] 58 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280706 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280706/1 /scratch/stefan/7769901/working/building/REAL300000280706 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/985 `/scratch/stefan/7769901/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280706.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280706 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 3, 3, 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] 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: [4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 52 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 44, 34, 23, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280706 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 3, 3, 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] 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, 30, 30, 30, 30, 22, 11, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 38, 38, 52, 52, 52, 52, 52, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 52 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280706 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280706 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280706/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280706/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280706 Building REAL300000280707 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280707' /scratch/stefan/7769901/working/building/REAL300000280707 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280707 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280707/0 /scratch/stefan/7769901/working/building/REAL300000280707 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/986 `/scratch/stefan/7769901/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280707 none CCN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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] 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: [4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 46, 46, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 1, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1] 69 rigid atoms, others: [32, 1, 2, 3, 4, 5, 43, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280707 none CCN1C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 46, 46, 46, 30, 11, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 69, 69, 69, 69, 69, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46] 69 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280707 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280707/1 /scratch/stefan/7769901/working/building/REAL300000280707 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/987 `/scratch/stefan/7769901/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280707.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280707 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 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: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 80 rigid atoms, others: [32, 1, 2, 3, 4, 5, 42, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280707 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 53, 53, 53, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 80, 80, 80, 80, 80, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 80 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 42, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280707 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280707 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280707/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280707/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280707 Building REAL300000280708 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280708' /scratch/stefan/7769901/working/building/REAL300000280708 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280708 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280708/0 /scratch/stefan/7769901/working/building/REAL300000280708 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/988 `/scratch/stefan/7769901/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1C(=O)[O-]) `REAL300000280708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280708 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 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] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 55, 55, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 21, 22, 23, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280708 none CC1=CC(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 4, 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] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 28, 10, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 28, 55, 55, 55, 55, 55, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 42, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280708 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280708 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280708/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280708 Building REAL300000280709 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280709' /scratch/stefan/7769901/working/building/REAL300000280709 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280709 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280709/0 /scratch/stefan/7769901/working/building/REAL300000280709 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/989 `/scratch/stefan/7769901/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280709 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 5, 13, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 13, 60, 60, 60, 60, 60, 60, 60, 60, 60] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280709 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280709 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280709 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280709/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280709 Building REAL300000280710 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280710' /scratch/stefan/7769901/working/building/REAL300000280710 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280710 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280710/0 /scratch/stefan/7769901/working/building/REAL300000280710 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/990 `/scratch/stefan/7769901/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F) `REAL300000280710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280710 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 81, 81, 42, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81] 81 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280710 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280710 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280710 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280710/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280710 Building REAL300000280711 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280711' /scratch/stefan/7769901/working/building/REAL300000280711 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280711 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280711/0 /scratch/stefan/7769901/working/building/REAL300000280711 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/991 `/scratch/stefan/7769901/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280711 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280711 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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, 27, 11, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51] 51 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280711 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280711/1 /scratch/stefan/7769901/working/building/REAL300000280711 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/992 `/scratch/stefan/7769901/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-]) `REAL300000280711.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280711 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 2, 2, 2, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280711 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 26, 11, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280711 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280711 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280711/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280711/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280711 Building REAL300000280712 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280712' /scratch/stefan/7769901/working/building/REAL300000280712 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280712 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280712/0 /scratch/stefan/7769901/working/building/REAL300000280712 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/993 `/scratch/stefan/7769901/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1) `REAL300000280712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280712 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 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, 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 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, 6, 6, 6, 23, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 37] set([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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280712 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 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, 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 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, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59] 59 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280712 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280712 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280712/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280712 Building REAL300000280713 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280713' /scratch/stefan/7769901/working/building/REAL300000280713 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280713 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280713/0 /scratch/stefan/7769901/working/building/REAL300000280713 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/994 `/scratch/stefan/7769901/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280713 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 21, 64, 64, 45, 64, 64, 64, 64, 64, 64, 64, 64, 64, 3, 3, 3, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64] 64 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 8, 9, 10, 11, 31] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280713 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 56, 64, 64, 64, 64, 64, 31, 11, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1] 64 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 28, 29, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280713 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280713/1 /scratch/stefan/7769901/working/building/REAL300000280713 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/995 `/scratch/stefan/7769901/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000280713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280713 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 1, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47] 47 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 31] set([0, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280713 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 47, 47, 47, 47, 47, 25, 11, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 34, 32, 33, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280713 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280713 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280713/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280713/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280713 Building REAL300000280714 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280714' /scratch/stefan/7769901/working/building/REAL300000280714 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280714 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280714/0 /scratch/stefan/7769901/working/building/REAL300000280714 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/996 `/scratch/stefan/7769901/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C(Cl)O1) `REAL300000280714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280714 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280714 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 29, 11, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280714 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280714 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280714/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280714 Building REAL300000280715 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280715' /scratch/stefan/7769901/working/building/REAL300000280715 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280715 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280715/0 /scratch/stefan/7769901/working/building/REAL300000280715 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/997 `/scratch/stefan/7769901/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1) `REAL300000280715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280715 none CCC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [6, 1, 1, 1, 1, 7, 7, 7, 23, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1] 101 rigid atoms, others: [1, 2, 3, 4, 41, 21, 22, 23, 24, 25, 26] set([0, 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, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280715 none CCC1=C(S(=O)(=O)[N-]C2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 83, 83, 35, 12, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83] 101 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 293 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280715 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280715/1 /scratch/stefan/7769901/working/building/REAL300000280715 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/998 `/scratch/stefan/7769901/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1) `REAL300000280715.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280715 none CCC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 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: [5, 1, 1, 1, 1, 4, 4, 4, 14, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1] 69 rigid atoms, others: [1, 2, 3, 4, 42, 21, 22, 23, 24, 25, 26] set([0, 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, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280715 none CCC1=C(S(=O)(=O)NC2=CC=C3C(=C2)CC2=CC=CC=C23)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 61, 61, 33, 11, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 69, 69, 69, 69, 69, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61] 69 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 32, 42, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280715 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280715 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280715/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280715/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280715 Building REAL300000280716 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280716' /scratch/stefan/7769901/working/building/REAL300000280716 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280716 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280716/0 /scratch/stefan/7769901/working/building/REAL300000280716 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/999 `/scratch/stefan/7769901/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280716 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 97, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 97, 97, 97, 97, 97, 97, 97, 29, 1, 1, 7, 7, 7, 1, 1] 201 rigid atoms, others: [32, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280716 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280716 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280716/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280716 Building REAL300000280717 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280717' /scratch/stefan/7769901/working/building/REAL300000280717 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280717 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280717/0 /scratch/stefan/7769901/working/building/REAL300000280717 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1000 `/scratch/stefan/7769901/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000280717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280717 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 121, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 121, 121, 121, 121, 121, 121, 121, 53, 1, 1, 1] 121 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280717 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280717 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280717/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280717 Building REAL300000280718 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280718' /scratch/stefan/7769901/working/building/REAL300000280718 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280718 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280718/0 /scratch/stefan/7769901/working/building/REAL300000280718 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1001 `/scratch/stefan/7769901/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280718 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 1, 1, 1, 7, 7, 7, 23, 65, 65, 65, 151, 151, 3, 3, 3, 1, 1, 5, 5, 1, 65, 151, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 26, 27, 30] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 628 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280718 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280718 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280718/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280718 Building REAL300000280719 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280719' /scratch/stefan/7769901/working/building/REAL300000280719 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280719 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280719/0 /scratch/stefan/7769901/working/building/REAL300000280719 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1002 `/scratch/stefan/7769901/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Br) `REAL300000280719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280719 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 51, 37, 37, 15, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 37, 1, 1, 1] 51 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280719 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280719 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280719/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280719 Building REAL300000280720 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280720' /scratch/stefan/7769901/working/building/REAL300000280720 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280720 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280720/0 /scratch/stefan/7769901/working/building/REAL300000280720 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1003 `/scratch/stefan/7769901/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280720 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 110, 110, 110, 196, 196, 4, 4, 4, 1, 1, 1, 110, 196, 196, 196, 196, 196, 196, 196] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280720 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280720 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280720/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280720 Building REAL300000280721 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280721' /scratch/stefan/7769901/working/building/REAL300000280721 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280721 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280721/0 /scratch/stefan/7769901/working/building/REAL300000280721 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1004 `/scratch/stefan/7769901/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(Br)C(C(=O)[O-])=C1) `REAL300000280721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280721 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(Br)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 45, 71, 45, 45, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 71, 71, 71, 71, 71, 71, 71, 45, 1, 1, 1] 71 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280721 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280721 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280721/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280721 Building REAL300000280722 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280722' /scratch/stefan/7769901/working/building/REAL300000280722 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280722 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280722/0 /scratch/stefan/7769901/working/building/REAL300000280722 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1005 `/scratch/stefan/7769901/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000280722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280722 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 29, 115, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 1, 1, 115, 115, 115, 115, 115, 115, 115, 29, 1, 1, 5, 5, 1, 1] 159 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 454 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280722 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280722 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280722/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280722 Building REAL300000280723 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280723' /scratch/stefan/7769901/working/building/REAL300000280723 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280723 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280723/0 /scratch/stefan/7769901/working/building/REAL300000280723 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1006 `/scratch/stefan/7769901/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280723 none CC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 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] 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, 2, 2, 2, 9, 47, 47, 47, 107, 107, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 47, 107, 107, 107, 107, 107, 107, 107, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 15, 16, 17, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280723 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280723 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280723/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280723 Building REAL300000280724 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280724' /scratch/stefan/7769901/working/building/REAL300000280724 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280724 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280724/0 /scratch/stefan/7769901/working/building/REAL300000280724 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1007 `/scratch/stefan/7769901/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl) `REAL300000280724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280724 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 53, 71, 53, 53, 17, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 53, 1, 1, 1] 71 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280724 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280724 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280724/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280724 Building REAL300000280725 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280725' /scratch/stefan/7769901/working/building/REAL300000280725 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280725 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280725/0 /scratch/stefan/7769901/working/building/REAL300000280725 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1008 `/scratch/stefan/7769901/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000280725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280725 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 95, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 95, 95, 95, 95, 95, 95, 95, 53, 1, 1, 1] 95 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280725 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280725 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280725/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280725 Building REAL300000280726 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280726' /scratch/stefan/7769901/working/building/REAL300000280726 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280726 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280726/0 /scratch/stefan/7769901/working/building/REAL300000280726 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1009 `/scratch/stefan/7769901/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Cl) `REAL300000280726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280726 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 81, 53, 53, 15, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 53, 1, 1] 81 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280726 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280726/1 /scratch/stefan/7769901/working/building/REAL300000280726 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1010 `/scratch/stefan/7769901/working/3D/1010' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Cl) `REAL300000280726.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280726 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 117, 135, 43, 117, 11, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 1, 1] 135 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280726 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280726 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280726/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280726/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280726 Building REAL300000280727 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280727' /scratch/stefan/7769901/working/building/REAL300000280727 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280727 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280727/0 /scratch/stefan/7769901/working/building/REAL300000280727 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1011 `/scratch/stefan/7769901/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1C) `REAL300000280727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280727 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 22, 22, 22, 31, 31, 1, 1, 2, 2, 2, 1, 1, 22, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280727 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280727 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280727/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280727 Building REAL300000280728 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280728' /scratch/stefan/7769901/working/building/REAL300000280728 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280728 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280728/0 /scratch/stefan/7769901/working/building/REAL300000280728 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1012 `/scratch/stefan/7769901/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000280728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280728 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 91, 125, 91, 91, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 91, 1, 1, 1] 125 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280728 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280728 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280728/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280728 Building REAL300000280729 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280729' /scratch/stefan/7769901/working/building/REAL300000280729 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280729 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280729/0 /scratch/stefan/7769901/working/building/REAL300000280729 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1013 `/scratch/stefan/7769901/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000280729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280729 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [47, 21, 47, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 13, 13, 1, 1, 47, 47, 47, 47, 47, 47, 47, 21, 1, 1, 6, 6, 9, 9, 1, 1] 113 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280729 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280729 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280729/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280729 Building REAL300000280730 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280730' /scratch/stefan/7769901/working/building/REAL300000280730 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280730 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280730/0 /scratch/stefan/7769901/working/building/REAL300000280730 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1014 `/scratch/stefan/7769901/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280730 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 7, 7, 7, 19, 47, 47, 47, 69, 69, 2, 2, 2, 1, 1, 1, 47, 69, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 246 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280730 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280730 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280730/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280730 Building REAL300000280731 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280731' /scratch/stefan/7769901/working/building/REAL300000280731 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280731 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280731/0 /scratch/stefan/7769901/working/building/REAL300000280731 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1015 `/scratch/stefan/7769901/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000280731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280731 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 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] 0 hydrogens 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, 23, 100, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 36, 36, 1, 1, 100, 100, 100, 100, 100, 100, 100, 23, 1, 1, 16, 16, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 461 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280731 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280731 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280731/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280731 Building REAL300000280732 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280732' /scratch/stefan/7769901/working/building/REAL300000280732 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280732 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280732/0 /scratch/stefan/7769901/working/building/REAL300000280732 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1016 `/scratch/stefan/7769901/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(N2CC(C(=O)[O-])CC2=O)C=C1) `REAL300000280732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280732 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(N2CC(C(=O)[O-])CC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 11, 11, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 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] 0 hydrogens 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, 26, 82, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 8, 8, 8, 1, 1, 82, 82, 82, 82, 82, 82, 82, 26, 1, 1, 8, 8, 8, 8, 8, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280732 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(N2CC(C(=O)[O-])CC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 11, 11, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 201, 124, 124, 27, 8, 1, 8, 8, 1, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 201, 201, 201, 201, 201, 201, 201, 124, 8, 8, 1, 1, 1, 1, 1, 8, 8] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280732 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280732 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280732/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280732 Building REAL300000280733 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280733' /scratch/stefan/7769901/working/building/REAL300000280733 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280733 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280733/0 /scratch/stefan/7769901/working/building/REAL300000280733 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1017 `/scratch/stefan/7769901/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Br)SC(C(=O)[O-])=C1) `REAL300000280733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280733 none CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Br)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 17, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 61, 93, 61, 61, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 93, 93, 93, 93, 93, 93, 93, 61, 1] 93 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280733 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280733/1 /scratch/stefan/7769901/working/building/REAL300000280733 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1018 `/scratch/stefan/7769901/working/3D/1018' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Br)SC(C(=O)[O-])=C1) `REAL300000280733.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280733 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Br)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 17, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 167, 173, 75, 167, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 173, 173, 173, 173, 173, 173, 173, 1] 173 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280733 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280733 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280733/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280733/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280733 Building REAL300000280734 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280734' /scratch/stefan/7769901/working/building/REAL300000280734 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280734 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280734/0 /scratch/stefan/7769901/working/building/REAL300000280734 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1019 `/scratch/stefan/7769901/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280734 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 2, 2, 1, 1, 1, 7, 7, 7, 21, 53, 53, 53, 67, 67, 2, 2, 2, 1, 2, 1, 53, 67, 67, 67, 67, 67, 67, 67] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 26] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 234 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280734 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280734 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280734/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280734 Building REAL300000280735 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280735' /scratch/stefan/7769901/working/building/REAL300000280735 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280735 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280735/0 /scratch/stefan/7769901/working/building/REAL300000280735 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1020 `/scratch/stefan/7769901/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1F) `REAL300000280735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280735 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 107, 201, 107, 107, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 201, 201, 107, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280735 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280735/1 /scratch/stefan/7769901/working/building/REAL300000280735 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1021 `/scratch/stefan/7769901/working/3D/1021' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1F) `REAL300000280735.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280735 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 201, 83, 163, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280735 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280735 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280735/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280735/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280735 Building REAL300000280736 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280736' /scratch/stefan/7769901/working/building/REAL300000280736 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280736 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280736/0 /scratch/stefan/7769901/working/building/REAL300000280736 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1022 `/scratch/stefan/7769901/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1) `REAL300000280736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280736 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 25, 109, 109, 109, 201, 201, 1, 2, 2, 2, 109, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 18, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280736 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280736 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280736/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280736 Building REAL300000280737 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280737' /scratch/stefan/7769901/working/building/REAL300000280737 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280737 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280737/0 /scratch/stefan/7769901/working/building/REAL300000280737 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1023 `/scratch/stefan/7769901/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280737 none CC1=CC(C)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 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, 3, 3, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 27, 27, 27, 61, 61, 1, 1, 1, 3, 3, 2, 2, 2, 1, 2, 2, 2, 27, 61, 61, 61, 61, 61, 61, 61, 1] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 24, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280737 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280737 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280737/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280737 Building REAL300000280738 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280738' /scratch/stefan/7769901/working/building/REAL300000280738 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280738 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280738/0 /scratch/stefan/7769901/working/building/REAL300000280738 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1024 `/scratch/stefan/7769901/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1OC) `REAL300000280738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280738 none COC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 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 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, 2, 9, 43, 43, 43, 123, 123, 1, 1, 1, 3, 3, 1, 1, 2, 4, 4, 4, 1, 43, 123, 123, 123, 123, 123, 123, 123, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 35, 20, 21, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280738 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280738 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280738/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280738 Building REAL300000280739 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280739' /scratch/stefan/7769901/working/building/REAL300000280739 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280739 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280739/0 /scratch/stefan/7769901/working/building/REAL300000280739 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1025 `/scratch/stefan/7769901/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280739 none COC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 137, 137, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 53, 137, 137, 137, 137, 137, 137, 137, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 16, 17, 18, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280739 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280739 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280739/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280739 Building REAL300000280740 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280740' /scratch/stefan/7769901/working/building/REAL300000280740 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280740 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280740/0 /scratch/stefan/7769901/working/building/REAL300000280740 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1026 `/scratch/stefan/7769901/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2) `REAL300000280740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280740 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 31, 27, 27, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280740 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280740 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280740/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280740 Building REAL300000280741 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280741' /scratch/stefan/7769901/working/building/REAL300000280741 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280741 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280741/0 /scratch/stefan/7769901/working/building/REAL300000280741 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1027 `/scratch/stefan/7769901/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C(C)C) `REAL300000280741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280741 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 19, 21, 19, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 33, 34, 35, 36, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 39, 8, 9, 38, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280741 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280741 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280741/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280741 Building REAL300000280742 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280742' /scratch/stefan/7769901/working/building/REAL300000280742 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280742 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280742/0 /scratch/stefan/7769901/working/building/REAL300000280742 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1028 `/scratch/stefan/7769901/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280742 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 23, 66, 66, 66, 118, 118, 6, 6, 6, 6, 6, 1, 1, 1, 66, 118, 118, 118, 118, 118, 118, 118] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27, 28] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 430 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280742 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280742 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280742/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280742 Building REAL300000280743 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280743' /scratch/stefan/7769901/working/building/REAL300000280743 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280743 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280743/0 /scratch/stefan/7769901/working/building/REAL300000280743 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1029 `/scratch/stefan/7769901/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280743 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 25, 75, 75, 75, 159, 159, 4, 4, 4, 1, 1, 2, 2, 1, 75, 159, 159, 159, 159, 159, 159, 159] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 25, 26, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280743 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280743 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280743/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280743 Building REAL300000280744 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280744' /scratch/stefan/7769901/working/building/REAL300000280744 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280744 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280744/0 /scratch/stefan/7769901/working/building/REAL300000280744 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1030 `/scratch/stefan/7769901/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1) `REAL300000280744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280744 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 27, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 27, 27, 27, 27, 21, 1, 1, 1] 27 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280744 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280744 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280744/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280744 Building REAL300000280745 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280745' /scratch/stefan/7769901/working/building/REAL300000280745 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280745 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280745/0 /scratch/stefan/7769901/working/building/REAL300000280745 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1031 `/scratch/stefan/7769901/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2) `REAL300000280745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280745 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 88, 98, 88, 88, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 98, 88, 1, 1, 1, 1, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280745 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280745 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280745/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280745 Building REAL300000280746 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280746' /scratch/stefan/7769901/working/building/REAL300000280746 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280746 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280746/0 /scratch/stefan/7769901/working/building/REAL300000280746 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1032 `/scratch/stefan/7769901/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1) `REAL300000280746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280746 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 99, 49, 49, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 99, 99, 99, 99, 99, 99, 99, 49, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 34, 35, 36, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280746 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280746 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280746/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280746 Building REAL300000280747 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280747' /scratch/stefan/7769901/working/building/REAL300000280747 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280747 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280747/0 /scratch/stefan/7769901/working/building/REAL300000280747 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1033 `/scratch/stefan/7769901/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]NC(=O)C(C)C)=C1) `REAL300000280747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280747 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]NC(=O)C(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 24, 80, 80, 80, 140, 140, 1, 2, 2, 2, 1, 2, 80, 140, 140, 140, 140, 140, 140, 140, 1] 280 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 34, 20, 24] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 507 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280747 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280747 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280747/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280747 Building REAL300000280748 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280748' /scratch/stefan/7769901/working/building/REAL300000280748 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280748 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280748/0 /scratch/stefan/7769901/working/building/REAL300000280748 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1034 `/scratch/stefan/7769901/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1) `REAL300000280748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280748 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 53, 104, 53, 53, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 104, 104, 104, 104, 104, 104, 104, 53, 1, 1, 1, 1, 1, 1, 1, 1] 104 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280748 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280748 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280748/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280748 Building REAL300000280749 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280749' /scratch/stefan/7769901/working/building/REAL300000280749 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280749 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280749/0 /scratch/stefan/7769901/working/building/REAL300000280749 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1035 `/scratch/stefan/7769901/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Cl)=C(Cl)C(C(=O)[O-])=C1) `REAL300000280749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280749 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Cl)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 53, 89, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 89, 89, 89, 89, 89, 89, 89, 53, 1, 1] 89 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280749 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280749/1 /scratch/stefan/7769901/working/building/REAL300000280749 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1036 `/scratch/stefan/7769901/working/3D/1036' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Cl)=C(Cl)C(C(=O)[O-])=C1) `REAL300000280749.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280749 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Cl)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 44, 19, 39, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280749 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280749 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280749/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280749/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280749 Building REAL300000280750 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280750' /scratch/stefan/7769901/working/building/REAL300000280750 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280750 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280750/0 /scratch/stefan/7769901/working/building/REAL300000280750 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1037 `/scratch/stefan/7769901/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl) `REAL300000280750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280750 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 66, 120, 66, 66, 17, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 120, 66, 1, 1] 120 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280750 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280750/1 /scratch/stefan/7769901/working/building/REAL300000280750 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1038 `/scratch/stefan/7769901/working/3D/1038' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl) `REAL300000280750.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280750 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 201, 43, 143, 11, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280750 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280750 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280750/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280750/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280750 Building REAL300000280751 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280751' /scratch/stefan/7769901/working/building/REAL300000280751 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280751 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280751/0 /scratch/stefan/7769901/working/building/REAL300000280751 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1039 `/scratch/stefan/7769901/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1) `REAL300000280751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280751 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 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] 0 hydrogens 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, 31, 97, 31, 31, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 17, 46, 46, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 31, 1, 1, 17, 17, 1] 201 rigid atoms, others: [34, 7, 10, 11, 12, 13, 14, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280751 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280751 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280751/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280751 Building REAL300000280752 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280752' /scratch/stefan/7769901/working/building/REAL300000280752 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280752 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280752/0 /scratch/stefan/7769901/working/building/REAL300000280752 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1040 `/scratch/stefan/7769901/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1OCC(=O)[O-]) `REAL300000280752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280752 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 104, 104, 1, 1, 1, 1, 8, 19, 44, 44, 2, 2, 2, 1, 33, 104, 104, 104, 104, 104, 104, 104, 1, 1, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 14, 15, 16, 17, 35, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280752 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280752 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280752/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280752 Building REAL300000280753 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280753' /scratch/stefan/7769901/working/building/REAL300000280753 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280753 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280753/0 /scratch/stefan/7769901/working/building/REAL300000280753 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1041 `/scratch/stefan/7769901/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCCCC(=O)[O-])C(F)=C1) `REAL300000280753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280753 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCCCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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] 0 hydrogens 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, 17, 47, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 10, 19, 22, 36, 36, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 17, 1, 1, 10, 10, 19, 19, 22, 22, 1] 201 rigid atoms, others: [32, 33, 7, 40, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280753 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280753 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280753/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280753 Building REAL300000280754 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280754' /scratch/stefan/7769901/working/building/REAL300000280754 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280754 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280754/0 /scratch/stefan/7769901/working/building/REAL300000280754 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1042 `/scratch/stefan/7769901/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280754 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 59, 59, 59, 73, 73, 2, 2, 2, 1, 1, 59, 73, 73, 73, 73, 73, 73, 73] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25] set([32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280754 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280754 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280754/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280754 Building REAL300000280755 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280755' /scratch/stefan/7769901/working/building/REAL300000280755 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280755 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280755/0 /scratch/stefan/7769901/working/building/REAL300000280755 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1043 `/scratch/stefan/7769901/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1OCCCC(=O)[O-]) `REAL300000280755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280755 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 3, 3, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 19, 57, 57, 1, 1, 1, 1, 4, 6, 15, 23, 37, 37, 2, 2, 2, 1, 19, 57, 57, 57, 57, 57, 57, 57, 1, 1, 6, 6, 15, 15, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 14, 15, 16, 17, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280755 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280755 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280755/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280755 Building REAL300000280756 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280756' /scratch/stefan/7769901/working/building/REAL300000280756 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280756 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280756/0 /scratch/stefan/7769901/working/building/REAL300000280756 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1044 `/scratch/stefan/7769901/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1) `REAL300000280756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280756 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 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] 0 hydrogens 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, 25, 81, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 21, 50, 50, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 25, 1, 1, 21, 21, 1] 201 rigid atoms, others: [34, 7, 10, 11, 12, 13, 14, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280756 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280756 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280756/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280756 Building REAL300000280757 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280757' /scratch/stefan/7769901/working/building/REAL300000280757 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280757 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280757/0 /scratch/stefan/7769901/working/building/REAL300000280757 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1045 `/scratch/stefan/7769901/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCCCC(=O)[O-])C(Cl)=C1) `REAL300000280757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280757 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OCCCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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] 0 hydrogens 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, 17, 53, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 18, 24, 42, 64, 64, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 17, 1, 1, 18, 18, 24, 24, 42, 42, 1] 201 rigid atoms, others: [32, 33, 7, 40, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280757 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280757 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280757/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280757 Building REAL300000280758 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280758' /scratch/stefan/7769901/working/building/REAL300000280758 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280758 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280758/0 /scratch/stefan/7769901/working/building/REAL300000280758 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1046 `/scratch/stefan/7769901/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280758 none CCOC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 37, 37, 37, 115, 115, 1, 1, 1, 3, 3, 28, 28, 28, 28, 28, 1, 1, 37, 115, 115, 115, 115, 115, 115, 115, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 17, 18, 19, 27, 28, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280758 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280758 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280758/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280758 Building REAL300000280759 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280759' /scratch/stefan/7769901/working/building/REAL300000280759 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280759 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280759/0 /scratch/stefan/7769901/working/building/REAL300000280759 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1047 `/scratch/stefan/7769901/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C(C(=O)[O-])S1) `REAL300000280759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280759 none CC1=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 35, 35, 35, 49, 49, 1, 1, 1, 1, 1, 1, 2, 2, 2, 35, 49, 49, 49, 49, 49, 49, 49, 1] 49 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 167 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280759 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280759 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280759/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280759 Building REAL300000280760 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280760' /scratch/stefan/7769901/working/building/REAL300000280760 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280760 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280760/0 /scratch/stefan/7769901/working/building/REAL300000280760 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1048 `/scratch/stefan/7769901/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1Cl) `REAL300000280760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280760 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 55, 73, 55, 55, 17, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 55, 1, 1] 73 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280760 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280760/1 /scratch/stefan/7769901/working/building/REAL300000280760 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1049 `/scratch/stefan/7769901/working/3D/1049' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1Cl) `REAL300000280760.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280760 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 107, 111, 48, 107, 11, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 1, 1] 111 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280760 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280760 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280760/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280760/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280760 Building REAL300000280761 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280761' /scratch/stefan/7769901/working/building/REAL300000280761 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280761 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280761/0 /scratch/stefan/7769901/working/building/REAL300000280761 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1050 `/scratch/stefan/7769901/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000280761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280761 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 45, 65, 45, 45, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 45, 1, 1, 1] 65 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280761 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280761 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280761/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280761 Building REAL300000280762 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280762' /scratch/stefan/7769901/working/building/REAL300000280762 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280762 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280762/0 /scratch/stefan/7769901/working/building/REAL300000280762 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1051 `/scratch/stefan/7769901/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Br) `REAL300000280762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280762 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 41, 56, 41, 41, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 41, 1, 1, 1] 56 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280762 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280762 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280762/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280762 Building REAL300000280763 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280763' /scratch/stefan/7769901/working/building/REAL300000280763 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280763 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280763/0 /scratch/stefan/7769901/working/building/REAL300000280763 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1052 `/scratch/stefan/7769901/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000280763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280763 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 53, 128, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 53, 1, 1, 1] 128 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280763 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280763 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280763/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280763 Building REAL300000280764 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280764' /scratch/stefan/7769901/working/building/REAL300000280764 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280764 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280764/0 /scratch/stefan/7769901/working/building/REAL300000280764 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1053 `/scratch/stefan/7769901/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000280764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280764 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 63, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 63, 63, 63, 63, 63, 63, 41, 1, 1, 1] 63 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280764 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280764 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280764/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280764 Building REAL300000280765 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280765' /scratch/stefan/7769901/working/building/REAL300000280765 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280765 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280765/0 /scratch/stefan/7769901/working/building/REAL300000280765 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1054 `/scratch/stefan/7769901/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1F) `REAL300000280765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280765 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 7, 7, 7, 25, 107, 107, 107, 127, 127, 1, 1, 2, 2, 2, 1, 1, 107, 127, 127, 127, 127, 127, 127, 127] 127 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 19, 20, 24, 25] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280765 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280765 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280765/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280765 Building REAL300000280766 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280766' /scratch/stefan/7769901/working/building/REAL300000280766 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280766 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280766/0 /scratch/stefan/7769901/working/building/REAL300000280766 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1055 `/scratch/stefan/7769901/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C(Cl)C=C1C(=O)[O-]) `REAL300000280766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280766 none COC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens 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, 5, 5, 5, 16, 57, 57, 57, 154, 154, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 57, 154, 154, 154, 154, 154, 154, 154, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 19, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280766 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280766 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280766/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280766 Building REAL300000280767 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280767' /scratch/stefan/7769901/working/building/REAL300000280767 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280767 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280767/0 /scratch/stefan/7769901/working/building/REAL300000280767 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1056 `/scratch/stefan/7769901/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000280767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280767 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 87, 119, 87, 87, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 87, 1, 1, 1] 119 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280767 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280767 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280767/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280767 Building REAL300000280768 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280768' /scratch/stefan/7769901/working/building/REAL300000280768 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280768 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280768/0 /scratch/stefan/7769901/working/building/REAL300000280768 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1057 `/scratch/stefan/7769901/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000280768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280768 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 53, 99, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99, 53, 1, 1, 1] 99 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280768 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280768 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280768/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280768 Building REAL300000280769 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280769' /scratch/stefan/7769901/working/building/REAL300000280769 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280769 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280769/0 /scratch/stefan/7769901/working/building/REAL300000280769 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1058 `/scratch/stefan/7769901/working/3D/1058' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280769 none CC1=C(Cl)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 59, 59, 59, 75, 75, 2, 2, 2, 1, 1, 59, 75, 75, 75, 75, 75, 75, 75] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25] set([32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280769 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280769 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280769/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280769 Building REAL300000280770 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280770' /scratch/stefan/7769901/working/building/REAL300000280770 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280770 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280770/0 /scratch/stefan/7769901/working/building/REAL300000280770 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1059 `/scratch/stefan/7769901/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Br)C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280770 none CC1=C(C(=O)[O-])C=C(Br)C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 17, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 77, 77, 77, 104, 104, 2, 2, 2, 1, 1, 77, 104, 104, 104, 104, 104, 104, 104] 104 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 24, 25] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280770 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280770 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280770/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280770 Building REAL300000280771 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280771' /scratch/stefan/7769901/working/building/REAL300000280771 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280771 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280771/0 /scratch/stefan/7769901/working/building/REAL300000280771 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1060 `/scratch/stefan/7769901/working/3D/1060' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1) `REAL300000280771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280771 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 50, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 32, 32, 49, 41, 1, 1, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [32, 37, 38, 7, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280771 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280771 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280771/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280771 Building REAL300000280772 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280772' /scratch/stefan/7769901/working/building/REAL300000280772 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280772 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280772/0 /scratch/stefan/7769901/working/building/REAL300000280772 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1061 `/scratch/stefan/7769901/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Br)=C1) `REAL300000280772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280772 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 53, 87, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 53, 1, 1, 1] 87 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280772 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280772 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280772/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280772 Building REAL300000280773 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280773' /scratch/stefan/7769901/working/building/REAL300000280773 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280773 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280773/0 /scratch/stefan/7769901/working/building/REAL300000280773 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1062 `/scratch/stefan/7769901/working/3D/1062' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1) `REAL300000280773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280773 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 55, 119, 55, 55, 9, 3, 1, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 119, 119, 119, 119, 55, 1, 1] 119 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280773 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280773/1 /scratch/stefan/7769901/working/building/REAL300000280773 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1063 `/scratch/stefan/7769901/working/3D/1063' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1) `REAL300000280773.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280773 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(F)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 50, 69, 21, 50, 7, 3, 1, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 69, 69, 69, 69, 1, 1] 69 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280773 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280773 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280773/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280773/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280773 Building REAL300000280774 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280774' /scratch/stefan/7769901/working/building/REAL300000280774 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280774 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280774/0 /scratch/stefan/7769901/working/building/REAL300000280774 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1064 `/scratch/stefan/7769901/working/3D/1064' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300000280774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280774 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 49, 53, 49, 49, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 49, 1, 1, 1] 53 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280774 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280774/1 /scratch/stefan/7769901/working/building/REAL300000280774 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1065 `/scratch/stefan/7769901/working/3D/1065' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300000280774.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280774 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 131, 135, 47, 131, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1] 135 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280774 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280774 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280774/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280774/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280774 Building REAL300000280775 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280775' /scratch/stefan/7769901/working/building/REAL300000280775 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280775 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280775/0 /scratch/stefan/7769901/working/building/REAL300000280775 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1066 `/scratch/stefan/7769901/working/3D/1066' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000280775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280775 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 230 conformations in input total number of sets (complete confs): 230 using faster count positions algorithm for large data unique positions, atoms: [115, 85, 115, 85, 85, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 85, 1, 1, 1, 2] 230 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 384 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280775 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280775/1 /scratch/stefan/7769901/working/building/REAL300000280775 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1067 `/scratch/stefan/7769901/working/3D/1067' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-]) `REAL300000280775.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280775 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 29, 49, 29, 29, 15, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 29, 1, 1, 1] 49 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280775 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280775 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280775/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280775/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280775 Building REAL300000280776 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280776' /scratch/stefan/7769901/working/building/REAL300000280776 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280776 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280776/0 /scratch/stefan/7769901/working/building/REAL300000280776 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1068 `/scratch/stefan/7769901/working/3D/1068' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280776 none CC1=C(Br)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 47, 47, 47, 107, 107, 1, 1, 1, 3, 3, 2, 2, 2, 1, 47, 107, 107, 107, 107, 107, 107, 107, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 16, 17, 18, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280776 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280776 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280776/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280776 Building REAL300000280777 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280777' /scratch/stefan/7769901/working/building/REAL300000280777 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280777 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280777/0 /scratch/stefan/7769901/working/building/REAL300000280777 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1069 `/scratch/stefan/7769901/working/3D/1069' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000280777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280777 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [69, 29, 69, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 69, 69, 69, 69, 69, 69, 69, 29, 1, 1, 2, 2, 1, 1] 81 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280777 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280777 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280777/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280777 Building REAL300000280778 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280778' /scratch/stefan/7769901/working/building/REAL300000280778 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280778 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280778/0 /scratch/stefan/7769901/working/building/REAL300000280778 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1070 `/scratch/stefan/7769901/working/3D/1070' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1) `REAL300000280778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280778 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 55, 119, 55, 55, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 119, 119, 119, 119, 55, 1, 1] 119 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280778 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280778/1 /scratch/stefan/7769901/working/building/REAL300000280778 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1071 `/scratch/stefan/7769901/working/3D/1071' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1) `REAL300000280778.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280778 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 47, 67, 20, 47, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 67, 67, 67, 67, 67, 67, 1, 1] 67 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280778 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280778 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280778/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280778/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280778 Building REAL300000280779 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280779' /scratch/stefan/7769901/working/building/REAL300000280779 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280779 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280779/0 /scratch/stefan/7769901/working/building/REAL300000280779 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1072 `/scratch/stefan/7769901/working/3D/1072' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280779 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 23, 63, 63, 63, 95, 95, 2, 2, 2, 1, 1, 1, 63, 95, 95, 95, 95, 95, 95, 95] 95 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23, 24, 25] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 340 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280779 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280779 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280779/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280779 Building REAL300000280780 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280780' /scratch/stefan/7769901/working/building/REAL300000280780 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280780 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280780/0 /scratch/stefan/7769901/working/building/REAL300000280780 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1073 `/scratch/stefan/7769901/working/3D/1073' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280780 none CC1=C(Br)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 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, 1, 1, 1, 7, 7, 7, 23, 61, 61, 61, 77, 77, 2, 2, 2, 1, 1, 61, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25] set([32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 254 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280780 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280780 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280780/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280780 Building REAL300000280781 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280781' /scratch/stefan/7769901/working/building/REAL300000280781 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280781 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280781/0 /scratch/stefan/7769901/working/building/REAL300000280781 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1074 `/scratch/stefan/7769901/working/3D/1074' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1F) `REAL300000280781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280781 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 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] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 49, 49, 49, 115, 115, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 49, 115, 115, 115, 115, 115, 115, 115, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 33, 14, 15, 16, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280781 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280781 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280781/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280781 Building REAL300000280782 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280782' /scratch/stefan/7769901/working/building/REAL300000280782 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280782 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280782/0 /scratch/stefan/7769901/working/building/REAL300000280782 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1075 `/scratch/stefan/7769901/working/3D/1075' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280782 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 63, 63, 63, 83, 83, 2, 2, 2, 1, 1, 1, 63, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 276 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280782 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280782 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280782/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280782 Building REAL300000280783 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280783' /scratch/stefan/7769901/working/building/REAL300000280783 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280783 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280783/0 /scratch/stefan/7769901/working/building/REAL300000280783 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1076 `/scratch/stefan/7769901/working/3D/1076' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1C) `REAL300000280783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280783 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 1, 5, 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, 3, 3, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 39, 39, 39, 59, 59, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 39, 59, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2] 59 rigid atoms, others: [0, 1, 2, 3, 4, 33, 14, 15, 16, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280783 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280783 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280783/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280783 Building REAL300000280784 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280784' /scratch/stefan/7769901/working/building/REAL300000280784 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280784 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280784/0 /scratch/stefan/7769901/working/building/REAL300000280784 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1077 `/scratch/stefan/7769901/working/3D/1077' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1) `REAL300000280784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280784 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 49, 53, 49, 49, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 49, 1, 1, 1] 53 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280784 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280784 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280784/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280784 Building REAL300000280785 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280785' /scratch/stefan/7769901/working/building/REAL300000280785 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280785 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280785/0 /scratch/stefan/7769901/working/building/REAL300000280785 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1078 `/scratch/stefan/7769901/working/3D/1078' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F) `REAL300000280785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280785 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 109, 136, 109, 109, 25, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 109, 1, 1] 136 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280785 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280785/1 /scratch/stefan/7769901/working/building/REAL300000280785 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1079 `/scratch/stefan/7769901/working/3D/1079' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F) `REAL300000280785.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280785 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 110, 117, 69, 110, 17, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 1, 1] 117 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280785 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280785 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280785/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280785/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280785 Building REAL300000280786 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280786' /scratch/stefan/7769901/working/building/REAL300000280786 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280786 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280786/0 /scratch/stefan/7769901/working/building/REAL300000280786 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1080 `/scratch/stefan/7769901/working/3D/1080' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Br)C=C(C(=O)[O-])S1) `REAL300000280786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280786 none CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Br)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 17, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 133, 193, 133, 133, 39, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 133, 1] 193 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280786 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280786/1 /scratch/stefan/7769901/working/building/REAL300000280786 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1081 `/scratch/stefan/7769901/working/3D/1081' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Br)C=C(C(=O)[O-])S1) `REAL300000280786.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280786 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Br)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 17, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 201, 104, 193, 29, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280786 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280786 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280786/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280786/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280786 Building REAL300000280787 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280787' /scratch/stefan/7769901/working/building/REAL300000280787 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280787 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280787/0 /scratch/stefan/7769901/working/building/REAL300000280787 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1082 `/scratch/stefan/7769901/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1C(=O)[O-]) `REAL300000280787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280787 none CC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 5, 1, 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, 3, 3, 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] 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 72, 72, 72, 90, 90, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 72, 90, 90, 90, 90, 90, 90, 90, 2, 2, 2] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 306 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280787 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280787 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280787/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280787 Building REAL300000280788 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280788' /scratch/stefan/7769901/working/building/REAL300000280788 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280788 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280788/0 /scratch/stefan/7769901/working/building/REAL300000280788 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1083 `/scratch/stefan/7769901/working/3D/1083' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280788 none CC1=CC(F)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 105, 105, 105, 201, 201, 1, 1, 1, 3, 3, 2, 2, 2, 1, 105, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 16, 17, 18, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280788 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280788 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280788/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280788 Building REAL300000280789 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280789' /scratch/stefan/7769901/working/building/REAL300000280789 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280789 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280789/0 /scratch/stefan/7769901/working/building/REAL300000280789 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1084 `/scratch/stefan/7769901/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1Cl) `REAL300000280789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280789 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 17, 53, 53, 53, 71, 71, 1, 1, 2, 2, 2, 1, 1, 53, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 19, 20, 24, 25] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280789 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280789 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280789/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280789 Building REAL300000280790 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280790' /scratch/stefan/7769901/working/building/REAL300000280790 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280790 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280790/0 /scratch/stefan/7769901/working/building/REAL300000280790 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1085 `/scratch/stefan/7769901/working/3D/1085' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]NC(=O)C(C)C)=C1) `REAL300000280790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280790 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]NC(=O)C(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 25, 109, 109, 109, 201, 201, 1, 2, 2, 2, 1, 109, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 20, 24] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280790 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280790 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280790/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280790 Building REAL300000280791 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280791' /scratch/stefan/7769901/working/building/REAL300000280791 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280791 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280791/0 /scratch/stefan/7769901/working/building/REAL300000280791 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1086 `/scratch/stefan/7769901/working/3D/1086' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280791 none COC1=CC(Br)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 45, 45, 45, 107, 107, 1, 1, 1, 3, 3, 4, 4, 4, 1, 45, 107, 107, 107, 107, 107, 107, 107, 1] 151 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 17, 18, 19, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280791 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280791 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280791/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280791 Building REAL300000280792 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280792' /scratch/stefan/7769901/working/building/REAL300000280792 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280792 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280792/0 /scratch/stefan/7769901/working/building/REAL300000280792 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1087) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1087 `/scratch/stefan/7769901/working/3D/1087' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280792 none CCC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 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, 3, 3, 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] 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: [6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 51, 51, 51, 107, 107, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 51, 107, 107, 107, 107, 107, 107, 107, 1] 177 rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 18, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 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/7769901/working/building/REAL300000280792 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280792 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280792/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280792 Building REAL300000280793 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280793' /scratch/stefan/7769901/working/building/REAL300000280793 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280793 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280793/0 /scratch/stefan/7769901/working/building/REAL300000280793 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1088) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1088 `/scratch/stefan/7769901/working/3D/1088' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Br) `REAL300000280793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280793 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 46, 88, 46, 46, 14, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 46, 1, 1] 88 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280793 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280793/1 /scratch/stefan/7769901/working/building/REAL300000280793 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1089) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1089 `/scratch/stefan/7769901/working/3D/1089' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Br) `REAL300000280793.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280793 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [198, 144, 198, 39, 144, 7, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 198, 198, 1, 1] 198 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 660 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280793 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280793 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280793/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280793/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280793 Building REAL300000280794 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280794' /scratch/stefan/7769901/working/building/REAL300000280794 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280794 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280794/0 /scratch/stefan/7769901/working/building/REAL300000280794 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1090) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1090 `/scratch/stefan/7769901/working/3D/1090' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1CC(=O)[O-]) `REAL300000280794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280794 none COC1=CC=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 135, 135, 1, 1, 1, 3, 7, 7, 4, 4, 4, 1, 1, 53, 135, 135, 135, 135, 135, 135, 135, 1, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 18, 35, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280794 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280794 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280794/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280794 Building REAL300000280795 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280795' /scratch/stefan/7769901/working/building/REAL300000280795 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280795 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280795/0 /scratch/stefan/7769901/working/building/REAL300000280795 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1091) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1091 `/scratch/stefan/7769901/working/3D/1091' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280795 none CC1=C(C(=O)[O-])C=C(Cl)C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 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, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 83, 83, 83, 107, 107, 2, 2, 2, 1, 1, 83, 107, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 24, 25] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280795 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280795 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280795/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280795 Building REAL300000280796 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280796' /scratch/stefan/7769901/working/building/REAL300000280796 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280796 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280796/0 /scratch/stefan/7769901/working/building/REAL300000280796 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1092) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1092 `/scratch/stefan/7769901/working/3D/1092' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C(F)(F)F)=C1) `REAL300000280796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280796 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 45, 55, 45, 45, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 55, 55, 55, 55, 55, 55, 55, 45, 1, 1, 1] 55 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280796 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280796/1 /scratch/stefan/7769901/working/building/REAL300000280796 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1093) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1093 `/scratch/stefan/7769901/working/3D/1093' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C(F)(F)F)=C1) `REAL300000280796.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280796 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 136, 142, 57, 136, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 142, 142, 142, 142, 142, 142, 142, 1, 1, 1] 142 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280796 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280796 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280796/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280796/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280796 Building REAL300000280797 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280797' /scratch/stefan/7769901/working/building/REAL300000280797 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280797 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280797/0 /scratch/stefan/7769901/working/building/REAL300000280797 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1094) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1094 `/scratch/stefan/7769901/working/3D/1094' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1Cl) `REAL300000280797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280797 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 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] 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, 3, 3, 3, 9, 47, 47, 47, 89, 89, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 47, 89, 89, 89, 89, 89, 89, 89, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 33, 14, 15, 16, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280797 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280797 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280797/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280797 Building REAL300000280798 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280798' /scratch/stefan/7769901/working/building/REAL300000280798 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280798 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280798/0 /scratch/stefan/7769901/working/building/REAL300000280798 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1095) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1095 `/scratch/stefan/7769901/working/3D/1095' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1) `REAL300000280798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280798 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.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'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 41, 65, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 65, 65, 65, 65, 65, 65, 41, 1, 1, 1] 65 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280798 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280798 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280798/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280798 Building REAL300000280799 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280799' /scratch/stefan/7769901/working/building/REAL300000280799 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280799 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280799/0 /scratch/stefan/7769901/working/building/REAL300000280799 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1096) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1096 `/scratch/stefan/7769901/working/3D/1096' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1Br) `REAL300000280799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280799 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 36, 36, 36, 52, 52, 1, 1, 2, 2, 2, 1, 1, 36, 52, 52, 52, 52, 52, 52, 52] 52 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 19, 20, 24, 25] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280799 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280799 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280799/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280799 Building REAL300000280800 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280800' /scratch/stefan/7769901/working/building/REAL300000280800 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280800 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280800/0 /scratch/stefan/7769901/working/building/REAL300000280800 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1097) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1097 `/scratch/stefan/7769901/working/3D/1097' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280800 none CCN1C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 49, 49, 49, 110, 110, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 49, 110, 110, 110, 110, 110, 110, 110, 1] 158 rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 19, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280800 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280800 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280800/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280800 Building REAL300000280801 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280801' /scratch/stefan/7769901/working/building/REAL300000280801 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280801 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280801/0 /scratch/stefan/7769901/working/building/REAL300000280801 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1098) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1098 `/scratch/stefan/7769901/working/3D/1098' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1CC(=O)[O-]) `REAL300000280801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280801 none CC1=CC(C)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 5, 1, 5, 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, 7, 7, 3, 3, 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] 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 24, 24, 24, 43, 43, 1, 1, 1, 1, 3, 7, 7, 2, 2, 2, 1, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 3, 3] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280801 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280801 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280801/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280801 Building REAL300000280802 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280802' /scratch/stefan/7769901/working/building/REAL300000280802 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280802 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280802/0 /scratch/stefan/7769901/working/building/REAL300000280802 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1099) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1099 `/scratch/stefan/7769901/working/3D/1099' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1Br) `REAL300000280802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280802 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 39, 55, 39, 39, 15, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 39, 1, 1] 55 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280802 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280802/1 /scratch/stefan/7769901/working/building/REAL300000280802 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1100) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1100 `/scratch/stefan/7769901/working/3D/1100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1Br) `REAL300000280802.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280802 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 100, 102, 35, 100, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 1, 1] 102 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280802 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280802 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280802/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280802/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280802 Building REAL300000280803 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280803' /scratch/stefan/7769901/working/building/REAL300000280803 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280803 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280803/0 /scratch/stefan/7769901/working/building/REAL300000280803 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1101) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1101 `/scratch/stefan/7769901/working/3D/1101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=C(Cl)C(C(=O)[O-])=C1) `REAL300000280803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280803 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(Br)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 17, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 53, 89, 53, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 89, 89, 89, 89, 89, 89, 89, 53, 1, 1] 89 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280803 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280803/1 /scratch/stefan/7769901/working/building/REAL300000280803 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1102) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1102 `/scratch/stefan/7769901/working/3D/1102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Br)=C(Cl)C(C(=O)[O-])=C1) `REAL300000280803.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280803 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(Br)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 17, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 44, 19, 40, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280803 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280803 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280803/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280803/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280803 Building REAL300000280804 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280804' /scratch/stefan/7769901/working/building/REAL300000280804 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280804 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280804/0 /scratch/stefan/7769901/working/building/REAL300000280804 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1103) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1103 `/scratch/stefan/7769901/working/3D/1103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C(Cl)=C1F) `REAL300000280804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280804 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 201, 125, 125, 25, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 125, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280804 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280804/1 /scratch/stefan/7769901/working/building/REAL300000280804 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1104) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1104 `/scratch/stefan/7769901/working/3D/1104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C(Cl)=C1F) `REAL300000280804.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280804 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(F)C(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 165, 194, 79, 165, 17, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 1] 194 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280804 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280804 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280804/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280804/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280804 Building REAL300000280805 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280805' /scratch/stefan/7769901/working/building/REAL300000280805 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280805 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280805/0 /scratch/stefan/7769901/working/building/REAL300000280805 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1105) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1105 `/scratch/stefan/7769901/working/3D/1105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC(F)(F)F) `REAL300000280805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280805 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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] 0 hydrogens 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, 90, 163, 90, 90, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 13, 13, 13, 163, 163, 163, 163, 163, 163, 163, 90, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280805 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280805/1 /scratch/stefan/7769901/working/building/REAL300000280805 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1106) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1106 `/scratch/stefan/7769901/working/3D/1106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC(F)(F)F) `REAL300000280805.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280805 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 119, 157, 73, 119, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 15, 15, 15, 157, 157, 157, 157, 157, 157, 157, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280805 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280805 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280805/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280805/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280805 Building REAL300000280806 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280806' /scratch/stefan/7769901/working/building/REAL300000280806 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280806 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280806/0 /scratch/stefan/7769901/working/building/REAL300000280806 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1107) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1107 `/scratch/stefan/7769901/working/3D/1107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280806 none CC1=C(Cl)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 49, 49, 49, 113, 113, 1, 1, 1, 3, 3, 2, 2, 2, 1, 49, 113, 113, 113, 113, 113, 113, 113, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 16, 17, 18, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280806 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280806 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280806/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280806 Building REAL300000280807 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280807' /scratch/stefan/7769901/working/building/REAL300000280807 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280807 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280807/0 /scratch/stefan/7769901/working/building/REAL300000280807 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1108) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1108 `/scratch/stefan/7769901/working/3D/1108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=C(C(C)(C)C)SC(C(=O)[O-])=C1) `REAL300000280807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280807 none CC(C)C(=O)N[N-]S(=O)(=O)C1=C(C(C)(C)C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 37, 41, 37, 37, 9, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 41, 41, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 41 rigid atoms, others: [7, 10, 11, 12, 16, 17, 18, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280807 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280807 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280807/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280807 Building REAL300000280808 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280808' /scratch/stefan/7769901/working/building/REAL300000280808 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280808 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280808/0 /scratch/stefan/7769901/working/building/REAL300000280808 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1109) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1109 `/scratch/stefan/7769901/working/3D/1109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Br) `REAL300000280808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280808 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 60, 35, 35, 13, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 35, 1, 1] 60 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280808 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280808/1 /scratch/stefan/7769901/working/building/REAL300000280808 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1110) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1110 `/scratch/stefan/7769901/working/3D/1110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Br) `REAL300000280808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280808 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(Cl)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 116, 127, 37, 116, 7, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 1, 1] 127 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280808 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280808 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280808/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280808/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280808 Building REAL300000280809 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280809' /scratch/stefan/7769901/working/building/REAL300000280809 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280809 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280809/0 /scratch/stefan/7769901/working/building/REAL300000280809 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1111) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1111 `/scratch/stefan/7769901/working/3D/1111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280809 none COC1=CC(Cl)=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 61, 61, 61, 146, 146, 1, 1, 1, 3, 3, 4, 4, 4, 1, 61, 146, 146, 146, 146, 146, 146, 146, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 17, 18, 19, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280809 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280809 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280809/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280809 Building REAL300000280810 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280810' /scratch/stefan/7769901/working/building/REAL300000280810 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280810 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280810/0 /scratch/stefan/7769901/working/building/REAL300000280810 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1112) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1112 `/scratch/stefan/7769901/working/3D/1112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1C(=O)[O-]) `REAL300000280810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280810 none CC1=CC(S(=O)(=O)[N-]NC(=O)C(C)C)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 56, 56, 56, 130, 130, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 56, 130, 130, 130, 130, 130, 130, 130, 1, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 14, 15, 16, 17, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280810 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280810 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280810/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280810 Building REAL300000280811 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280811' /scratch/stefan/7769901/working/building/REAL300000280811 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280811 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280811/0 /scratch/stefan/7769901/working/building/REAL300000280811 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1113) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1113 `/scratch/stefan/7769901/working/3D/1113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1C(=O)[O-]) `REAL300000280811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280811 none CC1=C(Br)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 5, 1, 1, 11, 11, 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, 3, 3, 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] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 72, 72, 72, 92, 92, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 72, 92, 92, 92, 92, 92, 92, 92, 2, 2, 2] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280811 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280811 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280811/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280811 Building REAL300000280812 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280812' /scratch/stefan/7769901/working/building/REAL300000280812 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280812 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280812/0 /scratch/stefan/7769901/working/building/REAL300000280812 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1114) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1114 `/scratch/stefan/7769901/working/3D/1114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-]) `REAL300000280812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280812 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 15, 31, 15, 15, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 15, 1, 1, 3, 3, 1] 37 rigid atoms, others: [32, 35, 7, 10, 11, 12, 13, 14, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280812 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280812 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280812/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280812 Building REAL300000280813 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280813' /scratch/stefan/7769901/working/building/REAL300000280813 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280813 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280813/0 /scratch/stefan/7769901/working/building/REAL300000280813 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1115) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1115 `/scratch/stefan/7769901/working/3D/1115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280813 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 4, 7, 6, 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, 3, 3, 1, 1, 1, 7, 7, 7, 19, 68, 68, 68, 118, 118, 2, 2, 2, 1, 1, 68, 118, 118, 118, 118, 118, 118, 118] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 25] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280813 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280813 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280813/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280813 Building REAL300000280814 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280814' /scratch/stefan/7769901/working/building/REAL300000280814 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280814 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280814/0 /scratch/stefan/7769901/working/building/REAL300000280814 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1116) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1116 `/scratch/stefan/7769901/working/3D/1116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-]) `REAL300000280814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280814 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 29, 29, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 29, 1, 1, 1] 31 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280814 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280814 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280814/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280814 Building REAL300000280815 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280815' /scratch/stefan/7769901/working/building/REAL300000280815 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280815 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280815/0 /scratch/stefan/7769901/working/building/REAL300000280815 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1117) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1117 `/scratch/stefan/7769901/working/3D/1117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000280815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280815 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 105, 201, 105, 105, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280815 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280815 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280815/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280815 Building REAL300000280816 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280816' /scratch/stefan/7769901/working/building/REAL300000280816 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280816 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280816/0 /scratch/stefan/7769901/working/building/REAL300000280816 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1118) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1118 `/scratch/stefan/7769901/working/3D/1118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-]) `REAL300000280816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280816 none CC1=C(F)C=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 47, 47, 47, 107, 107, 1, 1, 1, 3, 3, 2, 2, 2, 1, 47, 107, 107, 107, 107, 107, 107, 107, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 16, 17, 18, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280816 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280816 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280816/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280816 Building REAL300000280817 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280817' /scratch/stefan/7769901/working/building/REAL300000280817 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280817 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280817/0 /scratch/stefan/7769901/working/building/REAL300000280817 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1119) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1119 `/scratch/stefan/7769901/working/3D/1119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1) `REAL300000280817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280817 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 81, 45, 45, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 81, 81, 81, 81, 81, 81, 81, 45, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [32, 33, 34, 35, 36, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280817 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280817 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280817/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280817 Building REAL300000280818 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280818' /scratch/stefan/7769901/working/building/REAL300000280818 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280818 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280818/0 /scratch/stefan/7769901/working/building/REAL300000280818 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1120) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1120 `/scratch/stefan/7769901/working/3D/1120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C) `REAL300000280818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280818 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 122, 122, 122, 197, 197, 3, 3, 3, 1, 1, 1, 122, 197, 197, 197, 197, 197, 197, 197] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280818 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280818 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280818/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280818 Building REAL300000280819 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280819' /scratch/stefan/7769901/working/building/REAL300000280819 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280819 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280819/0 /scratch/stefan/7769901/working/building/REAL300000280819 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1121) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1121 `/scratch/stefan/7769901/working/3D/1121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000280819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280819 none CC(C)C(=O)N[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 89, 133, 89, 89, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 133, 133, 133, 133, 133, 133, 133, 89, 1] 133 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280819 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280819/1 /scratch/stefan/7769901/working/building/REAL300000280819 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1122) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1122 `/scratch/stefan/7769901/working/3D/1122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000280819.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280819 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 201, 101, 193, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280819 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280819 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280819/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280819/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280819 Building REAL300000280820 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280820' /scratch/stefan/7769901/working/building/REAL300000280820 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280820 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280820/0 /scratch/stefan/7769901/working/building/REAL300000280820 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1123) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1123 `/scratch/stefan/7769901/working/3D/1123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OC(F)(F)F)C(C(=O)[O-])=C1) `REAL300000280820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280820 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(OC(F)(F)F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 35, 90, 35, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 19, 19, 19, 1, 1, 3, 3, 1, 90, 90, 90, 90, 90, 90, 90, 35, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 10, 11, 12, 13, 14, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280820 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280820/1 /scratch/stefan/7769901/working/building/REAL300000280820 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1124) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1124 `/scratch/stefan/7769901/working/3D/1124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(OC(F)(F)F)C(C(=O)[O-])=C1) `REAL300000280820.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280820 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC=C(OC(F)(F)F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 73, 29, 48, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 20, 19, 20, 1, 1, 3, 3, 1, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280820 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280820 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280820/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280820/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280820 Building REAL300000280821 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280821' /scratch/stefan/7769901/working/building/REAL300000280821 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280821 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280821/0 /scratch/stefan/7769901/working/building/REAL300000280821 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1125) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1125 `/scratch/stefan/7769901/working/3D/1125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=C(C(=O)[O-])S1) `REAL300000280821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280821 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 17, 13, 13, 9, 4, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 13, 1, 3, 3, 3] 26 rigid atoms, others: [7, 10, 11, 12, 13, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280821 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280821/1 /scratch/stefan/7769901/working/building/REAL300000280821 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1126) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1126 `/scratch/stefan/7769901/working/3D/1126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=C(C(=O)[O-])S1) `REAL300000280821.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000280821 none CC(C)C(=O)[N-][N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [132, 120, 132, 53, 120, 13, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 7, 1, 1, 2, 2, 1, 132, 132, 132, 132, 132, 132, 132, 1, 7, 7, 7] 165 rigid atoms, others: [7, 10, 11, 12, 13, 17, 18, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280821 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280821 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280821/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280821/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280821 Building REAL300000280822 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280822' /scratch/stefan/7769901/working/building/REAL300000280822 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280822 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280822/0 /scratch/stefan/7769901/working/building/REAL300000280822 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1127) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1127 `/scratch/stefan/7769901/working/3D/1127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1) `REAL300000280822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280822 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 101, 29, 29, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 13, 17, 17, 13, 13, 1, 1, 101, 101, 101, 101, 101, 101, 101, 29, 1, 1, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [36, 37, 7, 10, 11, 12, 13, 14, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 409 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280822 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C(C2(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 201, 147, 147, 40, 13, 1, 12, 13, 1, 13, 13, 1, 1, 1, 3, 3, 1, 1, 13, 13, 201, 201, 201, 201, 201, 201, 201, 147, 13, 13, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 693 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280822 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280822 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280822/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280822 Building REAL300000280823 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280823' /scratch/stefan/7769901/working/building/REAL300000280823 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280823 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280823/0 /scratch/stefan/7769901/working/building/REAL300000280823 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1128) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1128 `/scratch/stefan/7769901/working/3D/1128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C2CC(C(=O)[O-])CC2=C1) `REAL300000280823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280823 none CC(C)C(=O)N[N-]S(=O)(=O)C1=CC=C2CC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 55, 107, 55, 55, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 55, 1, 1, 1, 1, 1, 1, 1, 1] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280823 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280823 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280823/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280823 Building REAL300000280824 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280824' /scratch/stefan/7769901/working/building/REAL300000280824 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280824 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280824/0 /scratch/stefan/7769901/working/building/REAL300000280824 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1129) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1129 `/scratch/stefan/7769901/working/3D/1129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C(C(=O)[O-])O1) `REAL300000280824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280824 none CCC1=C(S(=O)(=O)[N-]NC(=O)C(C)C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 7, 7, 7, 23, 102, 102, 102, 196, 196, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5, 102, 196, 196, 196, 196, 196, 196, 196, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 14, 15, 16, 17, 18, 19] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 729 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280824 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280824 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280824/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280824 Building REAL300000280825 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280825' /scratch/stefan/7769901/working/building/REAL300000280825 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280825 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280825/0 /scratch/stefan/7769901/working/building/REAL300000280825 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1130) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1130 `/scratch/stefan/7769901/working/3D/1130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280825 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 37, 37, 19, 1, 1, 1, 9, 37, 35, 35, 35, 35, 35, 1, 1, 7, 19, 19, 19, 1, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280825 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 87, 19, 19, 19, 19, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 19, 19, 75, 136, 142, 142, 142, 142, 142, 19, 19, 7, 1, 1, 1, 19, 136, 136, 136, 136, 136] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280825 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280825 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280825/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280825 Building REAL300000280826 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280826' /scratch/stefan/7769901/working/building/REAL300000280826 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280826 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280826/0 /scratch/stefan/7769901/working/building/REAL300000280826 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1131) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1131 `/scratch/stefan/7769901/working/3D/1131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1OCC) `REAL300000280826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280826 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 38, 37, 37, 37, 37, 37, 1, 1, 7, 17, 17, 17, 17, 1, 38, 38, 39, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 306 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280826 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 17, 17, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 83, 145, 150, 150, 150, 150, 150, 17, 17, 5, 1, 1, 1, 1, 17, 145, 145, 145, 145, 145] 201 rigid atoms, others: [33, 34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 819 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280826 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280826 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280826/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280826 Building REAL300000280827 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280827' /scratch/stefan/7769901/working/building/REAL300000280827 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280827 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280827/0 /scratch/stefan/7769901/working/building/REAL300000280827 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1132) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1132 `/scratch/stefan/7769901/working/3D/1132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280827 none CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 31, 32, 32, 32, 32, 32, 1, 1, 7, 25, 25, 25, 25, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280827 none CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 96, 25, 25, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 94, 152, 158, 158, 158, 158, 158, 25, 25, 9, 1, 1, 1, 1, 25, 152, 152, 152, 152, 152] 201 rigid atoms, others: [33, 34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 842 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280827 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280827/1 /scratch/stefan/7769901/working/building/REAL300000280827 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1133) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1133 `/scratch/stefan/7769901/working/3D/1133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280827.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280827 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 24, 32, 32, 32, 32, 32, 1, 1, 31, 31, 31, 31, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 259 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280827 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 104, 31, 31, 31, 31, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 81, 136, 170, 170, 170, 170, 170, 31, 31, 1, 1, 1, 1, 31, 136, 136, 136, 136, 136] 201 rigid atoms, others: [32, 33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 831 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280827 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280827 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280827/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280827/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280827 Building REAL300000280828 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280828' /scratch/stefan/7769901/working/building/REAL300000280828 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280828 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280828/0 /scratch/stefan/7769901/working/building/REAL300000280828 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1134) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1134 `/scratch/stefan/7769901/working/3D/1134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC) `REAL300000280828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280828 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 62, 1, 1, 1, 8, 20, 29, 29, 29, 29, 29, 1, 1, 47, 47, 47, 62, 62, 62, 1, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280828 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 47, 47, 47, 47, 19, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 47, 47, 47, 86, 121, 185, 185, 185, 185, 185, 47, 47, 1, 1, 1, 3, 3, 3, 47, 121, 121, 121, 121, 121] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 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: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280828 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280828/1 /scratch/stefan/7769901/working/building/REAL300000280828 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1135) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1135 `/scratch/stefan/7769901/working/3D/1135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC) `REAL300000280828.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280828 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 9, 36, 31, 31, 31, 31, 31, 1, 1, 7, 43, 43, 43, 43, 43, 43, 1, 36, 36, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280828 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 43, 43, 43, 43, 15, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 43, 43, 43, 113, 149, 186, 186, 186, 186, 186, 43, 43, 15, 1, 1, 1, 1, 1, 1, 43, 149, 149, 149, 149, 149] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280828 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280828 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280828/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280828/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280828 Building REAL300000280829 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280829' /scratch/stefan/7769901/working/building/REAL300000280829 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280829 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280829/0 /scratch/stefan/7769901/working/building/REAL300000280829 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1136) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1136 `/scratch/stefan/7769901/working/3D/1136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC) `REAL300000280829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280829 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 33, 33, 98, 98, 9, 9, 1, 1, 1, 9, 25, 26, 26, 26, 25, 25, 1, 1, 7, 9, 9, 33, 33, 9, 9, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 441 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280829 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 1, 1, 9, 9, 9, 58, 83, 87, 87, 87, 87, 87, 9, 9, 3, 1, 1, 5, 5, 1, 1, 9, 83, 83, 83, 83, 83] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 20, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 459 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280829 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280829/1 /scratch/stefan/7769901/working/building/REAL300000280829 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1137) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1137 `/scratch/stefan/7769901/working/3D/1137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC) `REAL300000280829.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280829 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 33, 33, 100, 100, 9, 9, 1, 1, 1, 9, 19, 24, 24, 24, 23, 23, 1, 1, 9, 9, 33, 33, 9, 9, 1, 19, 19, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280829 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 1, 1, 9, 9, 9, 44, 74, 99, 99, 99, 99, 99, 9, 9, 1, 1, 5, 5, 1, 1, 9, 74, 74, 74, 74, 74] 201 rigid atoms, others: [34, 35, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 513 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280829 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280829 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280829/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280829/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280829 Building REAL300000280830 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280830' /scratch/stefan/7769901/working/building/REAL300000280830 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280830 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280830/0 /scratch/stefan/7769901/working/building/REAL300000280830 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1138) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1138 `/scratch/stefan/7769901/working/3D/1138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280830 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 10, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 41, 40, 40, 40, 40, 40, 1, 1, 7, 23, 23, 23, 23, 23, 23, 1, 41, 41, 41, 41, 41] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280830 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 23, 23, 23, 23, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 94, 149, 165, 165, 165, 165, 165, 23, 23, 9, 1, 1, 2, 2, 2, 1, 23, 149, 149, 149, 149, 149] 201 rigid atoms, others: [34, 35, 39, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 861 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280830 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280830 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280830/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280830 Building REAL300000280831 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280831' /scratch/stefan/7769901/working/building/REAL300000280831 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280831 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280831/0 /scratch/stefan/7769901/working/building/REAL300000280831 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1139) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1139 `/scratch/stefan/7769901/working/3D/1139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC) `REAL300000280831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280831 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 25, 31, 31, 31, 31, 31, 1, 1, 30, 30, 30, 1, 25, 25, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280831 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 119, 30, 30, 30, 30, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 30, 30, 30, 84, 127, 173, 173, 173, 173, 173, 30, 30, 1, 1, 1, 30, 127, 127, 127, 127, 127] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 734 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280831 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280831/1 /scratch/stefan/7769901/working/building/REAL300000280831 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1140) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1140 `/scratch/stefan/7769901/working/3D/1140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC) `REAL300000280831.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280831 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 10, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 32, 40, 40, 40, 40, 40, 1, 1, 9, 27, 27, 27, 1, 32, 32, 33, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280831 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 108, 27, 27, 27, 27, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 27, 27, 27, 88, 135, 168, 168, 168, 168, 168, 27, 27, 7, 1, 1, 1, 27, 135, 135, 135, 135, 135] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280831 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280831 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280831/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280831/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280831 Building REAL300000280832 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280832' /scratch/stefan/7769901/working/building/REAL300000280832 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280832 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280832/0 /scratch/stefan/7769901/working/building/REAL300000280832 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1141) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1141 `/scratch/stefan/7769901/working/3D/1141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280832 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 11, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 41, 38, 38, 38, 38, 38, 1, 1, 7, 23, 23, 23, 1, 41, 41, 42, 42, 42] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280832 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 100, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 96, 151, 166, 166, 166, 166, 166, 23, 23, 9, 1, 1, 1, 23, 151, 151, 151, 151, 151] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280832 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280832/1 /scratch/stefan/7769901/working/building/REAL300000280832 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1142) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1142 `/scratch/stefan/7769901/working/3D/1142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280832.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280832 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 9, 30, 37, 37, 37, 37, 37, 1, 1, 29, 29, 29, 1, 30, 30, 31, 31, 31] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 299 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280832 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 108, 29, 29, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 83, 140, 175, 175, 175, 175, 175, 29, 29, 1, 1, 1, 29, 140, 140, 140, 140, 140] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 840 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280832 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280832 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280832/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280832/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280832 Building REAL300000280833 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280833' /scratch/stefan/7769901/working/building/REAL300000280833 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280833 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280833/0 /scratch/stefan/7769901/working/building/REAL300000280833 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1143) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1143 `/scratch/stefan/7769901/working/3D/1143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC) `REAL300000280833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280833 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 9, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 36, 41, 41, 41, 40, 40, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 1, 36, 36, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 347 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280833 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 122, 31, 31, 31, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 31, 31, 31, 90, 138, 175, 175, 175, 175, 175, 31, 31, 9, 1, 1, 2, 2, 2, 2, 2, 2, 31, 138, 138, 138, 138, 138] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 799 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280833 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280833/1 /scratch/stefan/7769901/working/building/REAL300000280833 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1144) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1144 `/scratch/stefan/7769901/working/3D/1144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC) `REAL300000280833.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280833 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 9, 25, 35, 35, 35, 34, 34, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 301 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280833 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 131, 40, 40, 40, 40, 12, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 90, 136, 181, 181, 181, 181, 181, 40, 40, 1, 1, 2, 2, 2, 2, 2, 2, 40, 136, 136, 136, 136, 136] 201 rigid atoms, others: [34, 35, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 751 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280833 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280833 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280833/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280833/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280833 Building REAL300000280834 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280834' /scratch/stefan/7769901/working/building/REAL300000280834 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280834 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280834/0 /scratch/stefan/7769901/working/building/REAL300000280834 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1145) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1145 `/scratch/stefan/7769901/working/3D/1145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1OCC) `REAL300000280834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280834 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 7, 21, 34, 34, 34, 34, 34, 1, 1, 46, 46, 46, 1, 21, 21, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280834 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 46, 46, 46, 46, 19, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 46, 46, 46, 96, 136, 195, 195, 195, 195, 195, 46, 46, 1, 1, 1, 46, 136, 136, 136, 136, 136] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280834 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280834 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280834/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280834 Building REAL300000280835 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280835' /scratch/stefan/7769901/working/building/REAL300000280835 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280835 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280835/0 /scratch/stefan/7769901/working/building/REAL300000280835 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1146) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1146 `/scratch/stefan/7769901/working/3D/1146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC) `REAL300000280835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280835 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 33, 48, 52, 52, 9, 9, 1, 1, 1, 9, 20, 14, 14, 14, 13, 13, 1, 1, 7, 9, 9, 33, 33, 48, 48, 9, 9, 1, 20, 20, 20, 20, 20] 148 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280835 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 43, 9, 9, 9, 9, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 7, 9, 9, 1, 1, 9, 9, 9, 55, 65, 50, 50, 50, 50, 50, 9, 9, 3, 1, 1, 4, 4, 7, 7, 1, 1, 9, 65, 65, 65, 65, 65] 148 rigid atoms, others: [35, 36, 8, 41, 42, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280835 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280835/1 /scratch/stefan/7769901/working/building/REAL300000280835 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1147) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1147 `/scratch/stefan/7769901/working/3D/1147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC) `REAL300000280835.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280835 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 22, 22, 40, 40, 9, 9, 1, 1, 1, 7, 9, 14, 14, 14, 13, 13, 1, 1, 9, 9, 22, 22, 22, 22, 9, 9, 1, 9, 9, 9, 9, 9] 93 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280835 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 37, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 1, 1, 9, 9, 9, 36, 36, 46, 46, 46, 46, 46, 9, 9, 1, 1, 6, 6, 6, 6, 1, 1, 9, 36, 36, 36, 36, 36] 93 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280835 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280835 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280835/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280835/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280835 Building REAL300000280836 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280836' /scratch/stefan/7769901/working/building/REAL300000280836 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280836 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280836/0 /scratch/stefan/7769901/working/building/REAL300000280836 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1148) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1148 `/scratch/stefan/7769901/working/3D/1148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1OCC) `REAL300000280836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280836 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 9, 24, 37, 37, 37, 37, 37, 1, 1, 50, 50, 1, 24, 24, 25, 25, 25] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 19, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280836 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 164, 50, 50, 50, 50, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 105, 144, 196, 196, 196, 196, 196, 50, 50, 1, 1, 50, 144, 144, 144, 144, 144] 201 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280836 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280836 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280836/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280836 Building REAL300000280837 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280837' /scratch/stefan/7769901/working/building/REAL300000280837 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280837 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280837/0 /scratch/stefan/7769901/working/building/REAL300000280837 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1149) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1149 `/scratch/stefan/7769901/working/3D/1149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC) `REAL300000280837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280837 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 34, 33, 33, 33, 33, 33, 1, 1, 9, 31, 31, 31, 31, 31, 31, 1, 34, 34, 35, 35, 35] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280837 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 31, 31, 31, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 31, 31, 31, 90, 136, 166, 166, 166, 166, 166, 31, 31, 9, 1, 1, 1, 2, 2, 2, 31, 136, 136, 136, 136, 136] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 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: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280837 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280837/1 /scratch/stefan/7769901/working/building/REAL300000280837 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1150) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1150 `/scratch/stefan/7769901/working/3D/1150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC) `REAL300000280837.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280837 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 9, 29, 31, 31, 31, 31, 31, 1, 1, 37, 37, 37, 37, 37, 37, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 296 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280837 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 123, 37, 37, 37, 37, 12, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 37, 37, 37, 92, 133, 175, 175, 175, 175, 175, 37, 37, 1, 1, 1, 2, 2, 2, 37, 133, 133, 133, 133, 133] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 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: 736 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280837 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280837 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280837/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280837/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280837 Building REAL300000280838 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280838' /scratch/stefan/7769901/working/building/REAL300000280838 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280838 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280838/0 /scratch/stefan/7769901/working/building/REAL300000280838 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1151) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1151 `/scratch/stefan/7769901/working/3D/1151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1OCC) `REAL300000280838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280838 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 33, 68, 70, 70, 9, 9, 1, 1, 1, 9, 12, 6, 6, 6, 6, 6, 1, 1, 7, 9, 9, 68, 68, 9, 9, 1, 12, 12, 12, 12, 12] 163 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 298 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280838 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 13, 13, 1, 1, 9, 9, 9, 29, 32, 23, 23, 23, 23, 23, 9, 9, 3, 1, 1, 11, 11, 1, 1, 9, 32, 32, 32, 32, 32] 163 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 20, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280838 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280838 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280838/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280838 Building REAL300000280839 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280839' /scratch/stefan/7769901/working/building/REAL300000280839 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280839 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280839/0 /scratch/stefan/7769901/working/building/REAL300000280839 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1152) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1152 `/scratch/stefan/7769901/working/3D/1152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280839 none CCOC1=CC=C(NS(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 7, 23, 30, 30, 30, 30, 30, 1, 1, 7, 27, 27, 27, 27, 27, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280839 none CCOC1=CC=C(NS(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 27, 27, 27, 27, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 92, 144, 166, 166, 166, 166, 166, 27, 27, 9, 1, 2, 2, 2, 1, 27, 144, 144, 144, 144, 144] 201 rigid atoms, others: [33, 37, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280839 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280839/1 /scratch/stefan/7769901/working/building/REAL300000280839 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1153) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1153 `/scratch/stefan/7769901/working/3D/1153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280839.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280839 none CCOC1=CC=C([N-]S(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 23, 26, 26, 26, 25, 25, 1, 1, 35, 35, 35, 35, 35, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280839 none CCOC1=CC=C([N-]S(=O)(=O)C2=CN(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 35, 35, 35, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 94, 143, 183, 183, 183, 183, 183, 35, 35, 1, 2, 2, 2, 1, 35, 143, 143, 143, 143, 143] 201 rigid atoms, others: [32, 36, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 838 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280839 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280839 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280839/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280839/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280839 Building REAL300000280840 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280840' /scratch/stefan/7769901/working/building/REAL300000280840 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280840 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280840/0 /scratch/stefan/7769901/working/building/REAL300000280840 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1154) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1154 `/scratch/stefan/7769901/working/3D/1154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(O)C=C2C)C=C1OCC) `REAL300000280840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280840 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(O)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [38, 10, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 28, 28, 28, 40, 40, 28, 28, 28, 28, 28, 1, 1, 1, 9, 30, 38, 38, 38, 38, 38, 1, 1, 8, 28, 56, 28, 28, 28, 28, 1, 30, 30, 31, 31, 31] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280840 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(O)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [166, 107, 28, 28, 28, 28, 9, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 28, 28, 28, 81, 125, 166, 166, 166, 166, 166, 28, 28, 9, 1, 2, 1, 2, 2, 2, 28, 125, 125, 125, 125, 125] 402 rigid atoms, others: [35, 37, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280840 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280840 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280840/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280840 Building REAL300000280841 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280841' /scratch/stefan/7769901/working/building/REAL300000280841 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280841 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280841/0 /scratch/stefan/7769901/working/building/REAL300000280841 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1155) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1155 `/scratch/stefan/7769901/working/3D/1155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=C(C(=O)[O-])S2)C=C1OCC) `REAL300000280841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280841 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=C(C(=O)[O-])S2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 9, 28, 42, 42, 42, 41, 41, 1, 1, 52, 52, 52, 52, 1, 28, 28, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 336 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280841 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=C(C(=O)[O-])S2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 11, 11, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 162, 52, 52, 52, 52, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 52, 112, 139, 195, 195, 195, 195, 195, 52, 52, 1, 2, 2, 2, 52, 139, 139, 139, 139, 139] 201 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 658 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280841 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280841 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280841/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280841 Building REAL300000280842 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280842' /scratch/stefan/7769901/working/building/REAL300000280842 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280842 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280842/0 /scratch/stefan/7769901/working/building/REAL300000280842 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1156) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1156 `/scratch/stefan/7769901/working/3D/1156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2C)C=C1OCC) `REAL300000280842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280842 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 22, 22, 22, 28, 28, 28, 42, 42, 28, 28, 28, 28, 28, 1, 1, 1, 9, 37, 38, 38, 38, 37, 37, 1, 1, 7, 28, 28, 28, 28, 28, 28, 28, 28, 1, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280842 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 116, 28, 28, 28, 28, 11, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 28, 28, 28, 70, 120, 179, 179, 179, 179, 179, 28, 28, 11, 1, 2, 2, 2, 1, 2, 2, 2, 28, 120, 120, 120, 120, 120] 201 rigid atoms, others: [35, 39, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280842 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280842 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280842/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280842 Building REAL300000280843 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280843' /scratch/stefan/7769901/working/building/REAL300000280843 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280843 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280843/0 /scratch/stefan/7769901/working/building/REAL300000280843 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1157) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1157 `/scratch/stefan/7769901/working/3D/1157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280843 none CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [30, 8, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 23, 30, 30, 30, 30, 30, 1, 1, 31, 31, 1, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 19, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280843 none CCOC1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [178, 104, 31, 31, 31, 31, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 91, 144, 178, 178, 178, 178, 178, 31, 31, 1, 1, 31, 144, 144, 144, 144, 144] 201 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280843 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280843/1 /scratch/stefan/7769901/working/building/REAL300000280843 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1158) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1158 `/scratch/stefan/7769901/working/3D/1158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280843.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280843 none CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 26, 34, 34, 34, 34, 34, 1, 1, 7, 27, 27, 1, 26, 26, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280843 none CCOC1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 109, 27, 27, 27, 27, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 94, 148, 170, 170, 170, 170, 170, 27, 27, 9, 1, 1, 27, 148, 148, 148, 148, 148] 201 rigid atoms, others: [32, 33, 8, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280843 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280843 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280843/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280843/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280843 Building REAL300000280844 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280844' /scratch/stefan/7769901/working/building/REAL300000280844 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280844 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280844/0 /scratch/stefan/7769901/working/building/REAL300000280844 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1159) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1159 `/scratch/stefan/7769901/working/3D/1159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OC)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280844 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 17, 17, 17, 17, 33, 17, 17, 29, 29, 17, 1, 1, 1, 10, 34, 31, 31, 31, 31, 31, 1, 1, 7, 17, 17, 33, 33, 33, 17, 1, 34, 34, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280844 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(OC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 79, 17, 17, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 17, 17, 17, 66, 106, 137, 137, 137, 137, 137, 17, 17, 5, 1, 1, 3, 3, 3, 1, 17, 106, 106, 106, 106, 106] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 15, 17, 18, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280844 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280844 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280844/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280844 Building REAL300000280845 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280845' /scratch/stefan/7769901/working/building/REAL300000280845 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280845 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280845/0 /scratch/stefan/7769901/working/building/REAL300000280845 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1160) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1160 `/scratch/stefan/7769901/working/3D/1160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC) `REAL300000280845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280845 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 41, 1, 1, 1, 9, 35, 45, 45, 45, 45, 45, 1, 1, 7, 19, 19, 19, 41, 41, 41, 41, 41, 1, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 421 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280845 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 92, 19, 19, 19, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 47, 101, 168, 168, 168, 168, 168, 19, 19, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 101, 101, 101, 101, 101] 201 rigid atoms, others: [35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 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: 796 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280845 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280845/1 /scratch/stefan/7769901/working/building/REAL300000280845 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1161) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1161 `/scratch/stefan/7769901/working/3D/1161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC) `REAL300000280845.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280845 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 10, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 55, 1, 1, 1, 9, 26, 40, 40, 40, 40, 40, 1, 1, 25, 25, 25, 55, 55, 55, 55, 55, 1, 26, 26, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280845 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2CC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 109, 25, 25, 25, 25, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 52, 92, 184, 184, 184, 184, 184, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 25, 92, 92, 92, 92, 92] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280845 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280845 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280845/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280845/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280845 Building REAL300000280846 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280846' /scratch/stefan/7769901/working/building/REAL300000280846 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280846 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280846/0 /scratch/stefan/7769901/working/building/REAL300000280846 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1162) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1162 `/scratch/stefan/7769901/working/3D/1162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280846 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 9, 24, 38, 38, 38, 38, 38, 1, 1, 49, 49, 49, 49, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280846 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 157, 49, 49, 49, 49, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 108, 141, 192, 192, 192, 192, 192, 49, 49, 2, 2, 2, 1, 49, 141, 141, 141, 141, 141] 201 rigid atoms, others: [35, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280846 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280846/1 /scratch/stefan/7769901/working/building/REAL300000280846 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1163) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1163 `/scratch/stefan/7769901/working/3D/1163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280846.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280846 none CCOC1=CC=C(NS(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 9, 27, 38, 38, 38, 38, 38, 1, 1, 7, 44, 44, 44, 44, 1, 27, 27, 28, 28, 28] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280846 none CCOC1=CC=C(NS(=O)(=O)C2=C(C)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 44, 44, 44, 44, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 112, 153, 187, 187, 187, 187, 187, 44, 44, 13, 2, 2, 2, 1, 44, 153, 153, 153, 153, 153] 201 rigid atoms, others: [36, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280846 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280846 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280846/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280846/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280846 Building REAL300000280847 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280847' /scratch/stefan/7769901/working/building/REAL300000280847 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280847 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280847/0 /scratch/stefan/7769901/working/building/REAL300000280847 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1164) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1164 `/scratch/stefan/7769901/working/3D/1164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC) `REAL300000280847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280847 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [38, 9, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 29, 38, 38, 38, 38, 38, 1, 1, 31, 31, 31, 31, 31, 62, 1, 29, 29, 29, 29, 29] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280847 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [178, 142, 31, 31, 31, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 117, 146, 178, 178, 178, 178, 178, 31, 31, 1, 2, 2, 2, 1, 2, 31, 146, 146, 146, 146, 146] 402 rigid atoms, others: [34, 38, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280847 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280847/1 /scratch/stefan/7769901/working/building/REAL300000280847 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1165) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1165 `/scratch/stefan/7769901/working/3D/1165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC) `REAL300000280847.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280847 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 34, 30, 30, 30, 29, 29, 1, 1, 7, 25, 25, 25, 25, 25, 50, 1, 34, 34, 35, 35, 35] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280847 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [165, 126, 25, 25, 25, 25, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 117, 159, 165, 165, 165, 165, 165, 25, 25, 7, 1, 2, 2, 2, 1, 2, 25, 159, 159, 159, 159, 159] 402 rigid atoms, others: [35, 39, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280847 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280847 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280847/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280847/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280847 Building REAL300000280848 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280848' /scratch/stefan/7769901/working/building/REAL300000280848 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280848 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280848/0 /scratch/stefan/7769901/working/building/REAL300000280848 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1166) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1166 `/scratch/stefan/7769901/working/3D/1166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC) `REAL300000280848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280848 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 25, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 33, 37, 37, 37, 36, 36, 1, 1, 9, 31, 31, 31, 31, 31, 1, 33, 33, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 320 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280848 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 115, 31, 31, 31, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 31, 31, 31, 89, 142, 173, 173, 173, 173, 173, 31, 31, 9, 1, 1, 2, 2, 2, 31, 142, 142, 142, 142, 142] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 821 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280848 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280848/1 /scratch/stefan/7769901/working/building/REAL300000280848 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1167) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1167 `/scratch/stefan/7769901/working/3D/1167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC) `REAL300000280848.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280848 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 9, 21, 36, 36, 36, 35, 35, 1, 1, 35, 35, 35, 35, 35, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280848 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(F)=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 130, 35, 35, 35, 35, 11, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 35, 35, 35, 89, 133, 177, 177, 177, 177, 177, 35, 35, 1, 1, 2, 2, 2, 35, 133, 133, 133, 133, 133] 201 rigid atoms, others: [34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280848 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280848 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280848/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280848/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280848 Building REAL300000280849 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280849' /scratch/stefan/7769901/working/building/REAL300000280849 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280849 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280849/0 /scratch/stefan/7769901/working/building/REAL300000280849 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1168) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1168 `/scratch/stefan/7769901/working/3D/1168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280849 none CCOC1=CC=C(NS(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 9, 28, 32, 32, 32, 31, 31, 1, 1, 7, 39, 39, 39, 39, 1, 28, 28, 28, 28, 28] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280849 none CCOC1=CC=C(NS(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 39, 39, 39, 39, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 39, 93, 137, 183, 183, 183, 183, 183, 39, 39, 13, 2, 2, 2, 1, 39, 137, 137, 137, 137, 137] 201 rigid atoms, others: [36, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280849 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280849/1 /scratch/stefan/7769901/working/building/REAL300000280849 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1169) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1169 `/scratch/stefan/7769901/working/3D/1169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280849.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280849 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 9, 25, 36, 36, 36, 36, 36, 1, 1, 45, 45, 45, 45, 1, 25, 25, 26, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280849 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(C)SC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 152, 45, 45, 45, 45, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 107, 142, 195, 195, 195, 195, 195, 45, 45, 2, 2, 2, 1, 45, 142, 142, 142, 142, 142] 201 rigid atoms, others: [35, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280849 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280849 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280849/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280849/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280849 Building REAL300000280850 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280850' /scratch/stefan/7769901/working/building/REAL300000280850 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280850 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280850/0 /scratch/stefan/7769901/working/building/REAL300000280850 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1170) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1170 `/scratch/stefan/7769901/working/3D/1170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC) `REAL300000280850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280850 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 20, 33, 33, 33, 33, 33, 1, 1, 21, 21, 21, 1, 20, 20, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280850 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 125, 21, 21, 21, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 101, 137, 171, 171, 171, 171, 171, 21, 21, 1, 1, 1, 21, 137, 137, 137, 137, 137] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 688 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280850 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280850/1 /scratch/stefan/7769901/working/building/REAL300000280850 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1171) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1171 `/scratch/stefan/7769901/working/3D/1171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC) `REAL300000280850.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280850 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 9, 28, 35, 35, 35, 35, 35, 1, 1, 7, 21, 21, 21, 1, 28, 28, 29, 29, 29] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 276 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280850 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 105, 21, 21, 21, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 100, 139, 161, 161, 161, 161, 161, 21, 21, 5, 1, 1, 1, 21, 139, 139, 139, 139, 139] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 722 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280850 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280850 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280850/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280850/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280850 Building REAL300000280851 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280851' /scratch/stefan/7769901/working/building/REAL300000280851 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280851 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280851/0 /scratch/stefan/7769901/working/building/REAL300000280851 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1172) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1172 `/scratch/stefan/7769901/working/3D/1172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC) `REAL300000280851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280851 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 37, 37, 21, 21, 21, 1, 1, 1, 7, 25, 27, 27, 27, 27, 27, 1, 1, 7, 21, 21, 21, 1, 25, 25, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280851 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 95, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 81, 128, 145, 145, 145, 145, 145, 21, 21, 9, 1, 1, 1, 21, 128, 128, 128, 128, 128] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 681 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280851 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280851/1 /scratch/stefan/7769901/working/building/REAL300000280851 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1173) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1173 `/scratch/stefan/7769901/working/3D/1173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC) `REAL300000280851.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280851 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 15, 15, 28, 28, 28, 28, 48, 48, 28, 28, 28, 1, 1, 1, 7, 21, 32, 32, 32, 31, 31, 1, 1, 28, 28, 28, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 313 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280851 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(F)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 97, 28, 28, 28, 28, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 28, 28, 28, 78, 108, 161, 161, 161, 161, 161, 28, 28, 1, 1, 1, 28, 108, 108, 108, 108, 108] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 655 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280851 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280851 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280851/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280851/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280851 Building REAL300000280852 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280852' /scratch/stefan/7769901/working/building/REAL300000280852 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280852 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280852/0 /scratch/stefan/7769901/working/building/REAL300000280852 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1174) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1174 `/scratch/stefan/7769901/working/3D/1174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1OCC) `REAL300000280852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280852 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [41, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 9, 26, 41, 41, 41, 41, 41, 1, 1, 53, 53, 1, 26, 26, 27, 27, 27] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 19, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280852 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])S2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [199, 163, 53, 53, 53, 53, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 113, 141, 199, 199, 199, 199, 199, 53, 53, 1, 1, 53, 141, 141, 141, 141, 141] 201 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 675 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280852 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280852 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280852/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280852 Building REAL300000280853 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280853' /scratch/stefan/7769901/working/building/REAL300000280853 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280853 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280853/0 /scratch/stefan/7769901/working/building/REAL300000280853 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1175) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1175 `/scratch/stefan/7769901/working/3D/1175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280853 none CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 32, 36, 36, 36, 35, 35, 1, 1, 7, 23, 23, 23, 1, 32, 32, 33, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 288 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280853 none CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 97, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 95, 154, 162, 162, 162, 162, 162, 23, 23, 9, 1, 1, 1, 23, 154, 154, 154, 154, 154] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 835 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280853 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280853/1 /scratch/stefan/7769901/working/building/REAL300000280853 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1176) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1176 `/scratch/stefan/7769901/working/3D/1176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280853.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280853 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 26, 39, 39, 39, 39, 39, 1, 1, 31, 31, 31, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 285 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280853 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 115, 31, 31, 31, 31, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 84, 141, 177, 177, 177, 177, 177, 31, 31, 1, 1, 1, 31, 141, 141, 141, 141, 141] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 810 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280853 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280853 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280853/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280853/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280853 Building REAL300000280854 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280854' /scratch/stefan/7769901/working/building/REAL300000280854 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280854 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280854/0 /scratch/stefan/7769901/working/building/REAL300000280854 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1177) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1177 `/scratch/stefan/7769901/working/3D/1177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2F)C=C1OCC) `REAL300000280854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280854 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 5, 17, 36, 36, 36, 35, 35, 1, 1, 49, 49, 49, 49, 49, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280854 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC(C)=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 49, 49, 49, 49, 19, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 49, 49, 49, 105, 148, 188, 188, 188, 188, 188, 49, 49, 1, 1, 2, 2, 2, 49, 148, 148, 148, 148, 148] 201 rigid atoms, others: [34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280854 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280854 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280854/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280854 Building REAL300000280855 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280855' /scratch/stefan/7769901/working/building/REAL300000280855 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280855 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280855/0 /scratch/stefan/7769901/working/building/REAL300000280855 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1178) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1178 `/scratch/stefan/7769901/working/3D/1178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC) `REAL300000280855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280855 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 43, 43, 24, 43, 43, 43, 43, 43, 43, 1, 1, 1, 9, 27, 33, 33, 33, 33, 33, 1, 1, 43, 43, 43, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280855 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 43, 43, 43, 43, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 43, 43, 111, 143, 190, 190, 190, 190, 190, 43, 43, 1, 1, 1, 43, 143, 143, 143, 143, 143] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280855 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280855/1 /scratch/stefan/7769901/working/building/REAL300000280855 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1179) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1179 `/scratch/stefan/7769901/working/3D/1179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC) `REAL300000280855.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280855 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 39, 39, 29, 39, 39, 39, 39, 39, 39, 1, 1, 1, 9, 33, 40, 40, 40, 39, 39, 1, 1, 7, 39, 39, 39, 1, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280855 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 137, 39, 39, 39, 39, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 108, 137, 183, 183, 183, 183, 183, 39, 39, 13, 1, 1, 1, 39, 137, 137, 137, 137, 137] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280855 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280855 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280855/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280855/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280855 Building REAL300000280856 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280856' /scratch/stefan/7769901/working/building/REAL300000280856 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280856 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280856/0 /scratch/stefan/7769901/working/building/REAL300000280856 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1180) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1180 `/scratch/stefan/7769901/working/3D/1180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC) `REAL300000280856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280856 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 9, 35, 37, 37, 37, 37, 37, 1, 1, 7, 21, 21, 21, 1, 35, 35, 36, 36, 36] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280856 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 98, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 88, 151, 167, 167, 167, 167, 167, 21, 21, 9, 1, 1, 1, 21, 151, 151, 151, 151, 151] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 855 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280856 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280856/1 /scratch/stefan/7769901/working/building/REAL300000280856 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1181) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1181 `/scratch/stefan/7769901/working/3D/1181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC) `REAL300000280856.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280856 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 8, 24, 37, 37, 37, 36, 36, 1, 1, 33, 33, 33, 1, 24, 24, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280856 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C(Cl)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 133, 33, 33, 33, 33, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 33, 33, 85, 126, 181, 181, 181, 181, 181, 33, 33, 1, 1, 1, 33, 126, 126, 126, 126, 126] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 669 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280856 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280856 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280856/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280856/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280856 Building REAL300000280857 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280857' /scratch/stefan/7769901/working/building/REAL300000280857 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280857 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280857/0 /scratch/stefan/7769901/working/building/REAL300000280857 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1182) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1182 `/scratch/stefan/7769901/working/3D/1182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1OCC) `REAL300000280857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280857 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 7, 15, 37, 37, 37, 37, 37, 1, 1, 48, 48, 48, 96, 1, 15, 15, 16, 16, 16] 402 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280857 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2O)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [181, 137, 48, 48, 48, 48, 15, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 48, 48, 48, 95, 123, 181, 181, 181, 181, 181, 48, 48, 1, 1, 1, 2, 48, 123, 123, 123, 123, 123] 402 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280857 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280857/1 /scratch/stefan/7769901/working/building/REAL300000280857 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1183) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1183 `/scratch/stefan/7769901/working/3D/1183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1OCC) `REAL300000280857.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280857 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 27, 41, 41, 41, 41, 41, 1, 1, 9, 25, 25, 25, 1, 27, 27, 28, 28, 28] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 37, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 305 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280857 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=CC=C2[O-])C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 112, 25, 25, 25, 25, 5, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 25, 25, 25, 84, 132, 168, 168, 168, 168, 168, 25, 25, 5, 1, 1, 1, 25, 132, 132, 132, 132, 132] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 749 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280857 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280857 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280857/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280857/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280857 Building REAL300000280858 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280858' /scratch/stefan/7769901/working/building/REAL300000280858 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280858 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280858/0 /scratch/stefan/7769901/working/building/REAL300000280858 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1184) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1184 `/scratch/stefan/7769901/working/3D/1184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC) `REAL300000280858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280858 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 11, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 13, 27, 27, 11, 11, 1, 1, 1, 8, 31, 27, 27, 27, 27, 27, 1, 1, 7, 11, 11, 13, 13, 11, 11, 1, 31, 31, 32, 32, 32] 127 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 267 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280858 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 54, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 11, 11, 11, 46, 85, 101, 101, 101, 101, 101, 11, 11, 5, 1, 1, 2, 2, 1, 1, 11, 85, 85, 85, 85, 85] 127 rigid atoms, others: [34, 35, 38, 39, 8, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 546 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280858 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280858/1 /scratch/stefan/7769901/working/building/REAL300000280858 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1185) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1185 `/scratch/stefan/7769901/working/3D/1185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC) `REAL300000280858.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280858 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 11, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 22, 29, 29, 12, 12, 1, 1, 1, 7, 27, 32, 32, 32, 31, 31, 1, 1, 12, 12, 22, 22, 12, 12, 1, 27, 27, 27, 27, 27] 146 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 294 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280858 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 56, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 12, 12, 12, 35, 68, 97, 97, 97, 97, 97, 12, 12, 1, 1, 2, 2, 1, 1, 12, 68, 68, 68, 68, 68] 146 rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 468 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280858 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280858 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280858/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280858/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280858 Building REAL300000280859 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280859' /scratch/stefan/7769901/working/building/REAL300000280859 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280859 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280859/0 /scratch/stefan/7769901/working/building/REAL300000280859 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1186) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1186 `/scratch/stefan/7769901/working/3D/1186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC) `REAL300000280859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280859 none CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 35, 36, 36, 36, 36, 36, 1, 1, 7, 23, 23, 23, 23, 23, 23, 1, 35, 35, 36, 36, 36] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280859 none CCOC1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 102, 23, 23, 23, 23, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 23, 23, 105, 154, 155, 155, 155, 155, 155, 23, 23, 5, 1, 1, 1, 2, 2, 2, 23, 154, 154, 154, 154, 154] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 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: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280859 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280859/1 /scratch/stefan/7769901/working/building/REAL300000280859 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1187) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1187 `/scratch/stefan/7769901/working/3D/1187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC) `REAL300000280859.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280859 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 9, 29, 38, 38, 38, 38, 38, 1, 1, 29, 29, 29, 29, 29, 29, 1, 29, 29, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280859 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 139, 29, 29, 29, 29, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 116, 155, 184, 184, 184, 184, 184, 29, 29, 1, 1, 1, 2, 2, 2, 29, 155, 155, 155, 155, 155] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 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: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280859 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280859 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280859/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280859/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280859 Building REAL300000280860 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280860' /scratch/stefan/7769901/working/building/REAL300000280860 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280860 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280860/0 /scratch/stefan/7769901/working/building/REAL300000280860 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1188) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1188 `/scratch/stefan/7769901/working/3D/1188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(F)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280860 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 37, 37, 19, 1, 1, 1, 9, 40, 40, 40, 40, 39, 39, 1, 1, 7, 19, 19, 19, 19, 19, 1, 40, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 372 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280860 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 83, 19, 19, 19, 19, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 19, 19, 71, 126, 155, 155, 155, 155, 155, 19, 19, 7, 1, 2, 2, 2, 1, 19, 126, 126, 126, 126, 126] 201 rigid atoms, others: [35, 39, 8, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 801 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280860 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280860 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280860/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280860 Building REAL300000280861 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280861' /scratch/stefan/7769901/working/building/REAL300000280861 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280861 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280861/0 /scratch/stefan/7769901/working/building/REAL300000280861 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1189) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1189 `/scratch/stefan/7769901/working/3D/1189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1OCC) `REAL300000280861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280861 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 21, 21, 21, 23, 23, 21, 21, 23, 23, 23, 23, 23, 1, 1, 1, 9, 29, 35, 35, 35, 35, 35, 1, 1, 7, 23, 23, 23, 23, 23, 23, 1, 29, 29, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280861 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 110, 23, 23, 23, 23, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 23, 103, 147, 166, 166, 166, 166, 166, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 147, 147, 147, 147, 147] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 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: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280861 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280861 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280861/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280861 Building REAL300000280862 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280862' /scratch/stefan/7769901/working/building/REAL300000280862 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280862 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280862/0 /scratch/stefan/7769901/working/building/REAL300000280862 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1190) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1190 `/scratch/stefan/7769901/working/3D/1190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280862 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 11, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 43, 34, 34, 34, 33, 33, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 1, 43, 43, 44, 44, 44] 195 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 307 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280862 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [157, 101, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 97, 155, 157, 157, 157, 157, 157, 23, 23, 9, 1, 2, 2, 2, 2, 2, 2, 1, 23, 155, 155, 155, 155, 155] 195 rigid atoms, others: [35, 8, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 847 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280862 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280862 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280862/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280862 Building REAL300000280863 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280863' /scratch/stefan/7769901/working/building/REAL300000280863 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280863 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280863/0 /scratch/stefan/7769901/working/building/REAL300000280863 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1191) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1191 `/scratch/stefan/7769901/working/3D/1191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2C)C=C1OCC) `REAL300000280863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280863 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 34, 35, 35, 35, 35, 35, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280863 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C)C(C(=O)[O-])=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 24, 24, 24, 24, 6, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 105, 156, 156, 156, 156, 156, 156, 24, 24, 6, 1, 1, 2, 2, 2, 2, 2, 2, 24, 156, 156, 156, 156, 156] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280863 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280863 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280863/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280863 Building REAL300000280864 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280864' /scratch/stefan/7769901/working/building/REAL300000280864 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280864 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280864/0 /scratch/stefan/7769901/working/building/REAL300000280864 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1192) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1192 `/scratch/stefan/7769901/working/3D/1192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC) `REAL300000280864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280864 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 44, 44, 44, 57, 57, 44, 44, 44, 44, 44, 1, 1, 1, 7, 21, 34, 34, 34, 34, 34, 1, 1, 44, 44, 44, 44, 44, 1, 21, 21, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280864 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 150, 44, 44, 44, 44, 18, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 44, 44, 44, 100, 131, 185, 185, 185, 185, 185, 44, 44, 1, 2, 2, 2, 1, 44, 131, 131, 131, 131, 131] 201 rigid atoms, others: [34, 38, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280864 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280864/1 /scratch/stefan/7769901/working/building/REAL300000280864 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1193) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1193 `/scratch/stefan/7769901/working/3D/1193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC) `REAL300000280864.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280864 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 9, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 35, 35, 35, 53, 53, 35, 35, 35, 35, 35, 1, 1, 1, 9, 31, 35, 35, 35, 34, 34, 1, 1, 7, 35, 35, 35, 35, 35, 1, 31, 31, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280864 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(C)C=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 132, 35, 35, 35, 35, 15, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 35, 35, 35, 88, 132, 172, 172, 172, 172, 172, 35, 35, 15, 1, 2, 2, 2, 1, 35, 132, 132, 132, 132, 132] 201 rigid atoms, others: [35, 39, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280864 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280864 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280864/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280864/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280864 Building REAL300000280865 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280865' /scratch/stefan/7769901/working/building/REAL300000280865 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280865 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280865/0 /scratch/stefan/7769901/working/building/REAL300000280865 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1194) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1194 `/scratch/stefan/7769901/working/3D/1194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2F)C=C1OCC) `REAL300000280865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280865 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 16, 16, 16, 29, 29, 29, 29, 29, 29, 50, 50, 29, 29, 1, 1, 1, 9, 23, 36, 36, 36, 36, 35, 1, 1, 29, 29, 29, 29, 29, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280865 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C)=CC(C(=O)[O-])=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 113, 29, 29, 29, 29, 10, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 29, 29, 29, 82, 107, 176, 176, 176, 176, 176, 29, 29, 1, 2, 2, 2, 1, 29, 107, 107, 107, 107, 107] 201 rigid atoms, others: [34, 38, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280865 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280865 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280865/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280865 Building REAL300000280866 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280866' /scratch/stefan/7769901/working/building/REAL300000280866 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280866 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280866/0 /scratch/stefan/7769901/working/building/REAL300000280866 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1195) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1195 `/scratch/stefan/7769901/working/3D/1195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280866 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 17, 17, 17, 17, 33, 17, 17, 17, 17, 17, 1, 1, 1, 9, 24, 31, 31, 31, 31, 31, 1, 1, 7, 17, 17, 33, 33, 33, 33, 33, 17, 1, 24, 24, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 306 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280866 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 17, 17, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 1, 1, 2, 2, 1, 17, 17, 17, 68, 88, 94, 94, 94, 94, 94, 17, 17, 5, 1, 1, 3, 3, 3, 3, 3, 1, 17, 88, 88, 88, 88, 88] 201 rigid atoms, others: [35, 36, 8, 42, 11, 12, 13, 14, 15, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 422 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280866 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280866 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280866/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280866 Building REAL300000280867 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280867' /scratch/stefan/7769901/working/building/REAL300000280867 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280867 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280867/0 /scratch/stefan/7769901/working/building/REAL300000280867 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1196) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1196 `/scratch/stefan/7769901/working/3D/1196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280867 none CCOC1=CC=C(NS(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 13, 13, 13, 24, 24, 24, 47, 24, 24, 24, 24, 24, 1, 1, 1, 7, 24, 25, 25, 25, 25, 25, 1, 1, 7, 24, 47, 47, 47, 47, 47, 24, 1, 24, 24, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280867 none CCOC1=CC=C(NS(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 9, 2, 1, 2, 2, 1, 1, 1, 1, 4, 1, 1, 2, 2, 1, 24, 24, 24, 76, 101, 107, 107, 107, 107, 107, 24, 24, 9, 1, 4, 4, 4, 4, 4, 1, 24, 101, 101, 101, 101, 101] 201 rigid atoms, others: [34, 8, 11, 12, 13, 14, 16, 17, 20, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280867 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280867/1 /scratch/stefan/7769901/working/building/REAL300000280867 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1197) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1197 `/scratch/stefan/7769901/working/3D/1197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280867.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280867 none CCOC1=CC=C([N-]S(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 15, 15, 27, 27, 27, 63, 27, 27, 27, 27, 27, 1, 1, 1, 7, 24, 33, 33, 33, 33, 33, 1, 1, 27, 63, 63, 63, 63, 63, 27, 1, 24, 24, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 435 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280867 none CCOC1=CC=C([N-]S(=O)(=O)C2=CN(CC)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 1, 1, 11, 11, 1, 1, 1, 12, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 27, 27, 27, 27, 9, 3, 1, 3, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 27, 27, 27, 55, 91, 119, 119, 119, 119, 119, 27, 27, 1, 4, 4, 4, 4, 4, 1, 27, 91, 91, 91, 91, 91] 201 rigid atoms, others: [33, 39, 8, 11, 12, 13, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 512 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280867 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280867 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280867/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280867/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280867 Building REAL300000280868 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280868' /scratch/stefan/7769901/working/building/REAL300000280868 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280868 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280868/0 /scratch/stefan/7769901/working/building/REAL300000280868 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1198) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1198 `/scratch/stefan/7769901/working/3D/1198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(C)=C2)C=C1OCC) `REAL300000280868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280868 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(C)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 37, 37, 21, 21, 21, 1, 1, 1, 9, 25, 27, 27, 27, 27, 27, 1, 1, 7, 21, 21, 21, 21, 21, 21, 1, 25, 25, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280868 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C(C)=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 94, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 78, 124, 146, 146, 146, 146, 146, 21, 21, 9, 1, 1, 2, 2, 2, 1, 21, 124, 124, 124, 124, 124] 201 rigid atoms, others: [34, 35, 39, 8, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 665 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280868 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280868 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280868/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280868 Building REAL300000280869 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280869' /scratch/stefan/7769901/working/building/REAL300000280869 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280869 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280869/0 /scratch/stefan/7769901/working/building/REAL300000280869 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1199) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1199 `/scratch/stefan/7769901/working/3D/1199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2C)C=C1OCC) `REAL300000280869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280869 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 1, 1, 1, 9, 34, 37, 37, 37, 37, 37, 1, 1, 7, 23, 23, 23, 23, 23, 1, 34, 34, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280869 none CCOC1=CC=C(NS(=O)(=O)C2=CC(C(=O)[O-])=C(F)C=C2C)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 103, 23, 23, 23, 23, 7, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 23, 23, 23, 67, 120, 159, 159, 159, 159, 159, 23, 23, 7, 1, 1, 2, 2, 2, 23, 120, 120, 120, 120, 120] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280869 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280869 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280869/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280869 Building REAL300000280870 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280870' /scratch/stefan/7769901/working/building/REAL300000280870 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280870 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280870/0 /scratch/stefan/7769901/working/building/REAL300000280870 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1200) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1200 `/scratch/stefan/7769901/working/3D/1200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1OCC) `REAL300000280870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280870 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 25, 25, 43, 43, 25, 25, 1, 1, 1, 9, 21, 39, 39, 39, 39, 39, 1, 1, 25, 25, 25, 1, 21, 21, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280870 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2F)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 118, 25, 25, 25, 25, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 25, 25, 25, 88, 119, 172, 172, 172, 172, 172, 25, 25, 1, 1, 1, 25, 119, 119, 119, 119, 119] 201 rigid atoms, others: [33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280870 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280870 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280870/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280870 Building REAL300000280871 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280871' /scratch/stefan/7769901/working/building/REAL300000280871 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280871 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280871/0 /scratch/stefan/7769901/working/building/REAL300000280871 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1201) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1201 `/scratch/stefan/7769901/working/3D/1201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280871 none CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 39, 37, 37, 37, 37, 37, 1, 1, 7, 23, 23, 23, 23, 23, 1, 39, 39, 39, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280871 none CCOC1=CC=C(NS(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 101, 23, 23, 23, 23, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 101, 160, 158, 158, 158, 158, 158, 23, 23, 9, 1, 2, 2, 2, 1, 23, 160, 160, 160, 160, 160] 201 rigid atoms, others: [35, 39, 8, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 837 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280871 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280871/1 /scratch/stefan/7769901/working/building/REAL300000280871 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1202) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1202 `/scratch/stefan/7769901/working/3D/1202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000280871.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280871 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 9, 29, 35, 35, 35, 35, 35, 1, 1, 29, 29, 29, 29, 29, 1, 29, 29, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280871 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(F)=C(C)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 111, 29, 29, 29, 29, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 86, 139, 170, 170, 170, 170, 170, 29, 29, 1, 2, 2, 2, 1, 29, 139, 139, 139, 139, 139] 201 rigid atoms, others: [34, 38, 8, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 826 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280871 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280871 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280871/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280871/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280871 Building REAL300000280872 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280872' /scratch/stefan/7769901/working/building/REAL300000280872 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280872 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280872/0 /scratch/stefan/7769901/working/building/REAL300000280872 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1203) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1203 `/scratch/stefan/7769901/working/3D/1203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1OCC) `REAL300000280872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280872 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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 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, 7, 19, 19, 19, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 6, 17, 33, 33, 33, 32, 32, 1, 1, 58, 58, 58, 1, 17, 17, 18, 18, 18] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 35, 20, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280872 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 162, 58, 58, 58, 58, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 112, 142, 190, 190, 190, 190, 190, 58, 58, 1, 1, 1, 58, 142, 142, 142, 142, 142] 201 rigid atoms, others: [32, 33, 34, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280872 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280872 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280872/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280872 Building REAL300000280873 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280873' /scratch/stefan/7769901/working/building/REAL300000280873 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280873 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280873/0 /scratch/stefan/7769901/working/building/REAL300000280873 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1204) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1204 `/scratch/stefan/7769901/working/3D/1204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC) `REAL300000280873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280873 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 38, 38, 23, 38, 38, 38, 38, 38, 38, 44, 1, 1, 1, 9, 23, 35, 35, 35, 34, 34, 1, 1, 38, 38, 38, 44, 44, 44, 1, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280873 none CCOC1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 38, 38, 38, 38, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 38, 38, 38, 95, 133, 197, 197, 197, 197, 197, 38, 38, 1, 1, 1, 3, 3, 3, 38, 133, 133, 133, 133, 133] 201 rigid atoms, others: [34, 35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 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: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280873 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280873/1 /scratch/stefan/7769901/working/building/REAL300000280873 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1205) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1205 `/scratch/stefan/7769901/working/3D/1205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC) `REAL300000280873.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280873 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 21, 21, 31, 31, 27, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 33, 36, 36, 36, 35, 35, 1, 1, 7, 31, 31, 31, 31, 31, 31, 1, 33, 33, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280873 none CCOC1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2OC)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 132, 31, 31, 31, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 31, 31, 31, 103, 144, 174, 174, 174, 174, 174, 31, 31, 9, 1, 1, 1, 2, 2, 2, 31, 144, 144, 144, 144, 144] 201 rigid atoms, others: [35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 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: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280873 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280873 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280873/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280873/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280873 Building REAL300000280874 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280874' /scratch/stefan/7769901/working/building/REAL300000280874 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280874 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280874/0 /scratch/stefan/7769901/working/building/REAL300000280874 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1206) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1206 `/scratch/stefan/7769901/working/3D/1206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280874 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [35, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 9, 23, 35, 35, 35, 35, 35, 1, 1, 49, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 20, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35, 36, 37, 38]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280874 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(Cl)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [190, 147, 49, 49, 49, 49, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 99, 139, 190, 190, 190, 190, 190, 49, 49, 1, 49, 139, 139, 139, 139, 139] 201 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280874 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280874 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280874/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280874 Building REAL300000280875 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280875' /scratch/stefan/7769901/working/building/REAL300000280875 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280875 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280875/0 /scratch/stefan/7769901/working/building/REAL300000280875 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1207) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1207 `/scratch/stefan/7769901/working/3D/1207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N-]S(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280875 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 39, 39, 58, 39, 39, 39, 39, 39, 39, 1, 1, 1, 9, 25, 39, 39, 39, 39, 39, 1, 1, 58, 58, 58, 58, 58, 39, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280875 none CCOC1=CC=C([N-]S(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 39, 39, 39, 39, 17, 7, 1, 7, 7, 1, 1, 1, 5, 1, 1, 1, 2, 2, 1, 39, 39, 39, 84, 107, 185, 185, 185, 185, 185, 39, 39, 5, 5, 5, 5, 5, 1, 39, 107, 107, 107, 107, 107] 201 rigid atoms, others: [38, 8, 11, 12, 13, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 658 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280875 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280875/1 /scratch/stefan/7769901/working/building/REAL300000280875 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1208) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1208 `/scratch/stefan/7769901/working/3D/1208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(NS(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC) `REAL300000280875.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280875 none CCOC1=CC=C(NS(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 39, 39, 62, 39, 39, 39, 39, 39, 39, 1, 1, 1, 9, 29, 35, 35, 35, 35, 35, 1, 1, 7, 62, 62, 62, 62, 62, 39, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280875 none CCOC1=CC=C(NS(=O)(=O)C2=C(CC)OC(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 12, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 132, 39, 39, 39, 39, 13, 5, 1, 5, 5, 1, 1, 1, 6, 1, 1, 1, 2, 2, 1, 39, 39, 39, 83, 121, 179, 179, 179, 179, 179, 39, 39, 13, 6, 6, 6, 6, 6, 1, 39, 121, 121, 121, 121, 121] 201 rigid atoms, others: [39, 8, 11, 12, 13, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280875 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280875 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280875/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280875/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280875 Building REAL300000280876 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280876' /scratch/stefan/7769901/working/building/REAL300000280876 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280876 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280876/0 /scratch/stefan/7769901/working/building/REAL300000280876 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1209) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1209 `/scratch/stefan/7769901/working/3D/1209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280876 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 15, 84, 84, 84, 84, 110, 110, 21, 21, 1, 13, 13, 13, 1, 1, 1, 9, 21, 21, 84, 84, 84, 21, 21, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 41, 26, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280876 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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: [90, 90, 21, 90, 21, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 21, 90, 90, 90, 21, 21, 21, 4, 1, 1, 7, 7, 7, 1, 1, 21] 201 rigid atoms, others: [34, 35, 39, 40, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280876 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280876/1 /scratch/stefan/7769901/working/building/REAL300000280876 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1210) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1210 `/scratch/stefan/7769901/working/3D/1210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280876.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280876 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 15, 15, 96, 96, 96, 96, 131, 131, 25, 25, 1, 12, 12, 12, 1, 1, 1, 25, 25, 96, 96, 96, 25, 25, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 40, 26, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280876 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 91, 25, 25, 25, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 25, 91, 91, 91, 25, 25, 25, 1, 1, 7, 7, 7, 1, 1, 25] 201 rigid atoms, others: [33, 34, 38, 39, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280876 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280876 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280876/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280876/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280876 Building REAL300000280877 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280877' /scratch/stefan/7769901/working/building/REAL300000280877 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280877 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280877/0 /scratch/stefan/7769901/working/building/REAL300000280877 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1211) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1211 `/scratch/stefan/7769901/working/3D/1211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCC3=C2)C=C1) `REAL300000280877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280877 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 22, 22, 22, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 4, 4, 4, 1, 1, 8, 38, 38, 38, 38, 38, 38, 38, 1, 1] 68 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 39, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280877 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 17, 68, 13, 38, 38, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 68, 68, 68, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 38, 38] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280877 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280877/1 /scratch/stefan/7769901/working/building/REAL300000280877 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1212) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1212 `/scratch/stefan/7769901/working/3D/1212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCC3=C2)C=C1) `REAL300000280877.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280877 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 24, 24, 24, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 41, 41, 41, 1, 1] 71 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 39, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280877 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 17, 71, 16, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 71, 71, 71, 41, 41, 1, 1, 1, 1, 1, 1, 1, 41, 41] 71 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 38, 39]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280877 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280877 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280877/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280877/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280877 Building REAL300000280878 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280878' /scratch/stefan/7769901/working/building/REAL300000280878 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280878 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280878/0 /scratch/stefan/7769901/working/building/REAL300000280878 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1213) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1213 `/scratch/stefan/7769901/working/3D/1213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CC2)C=C1) `REAL300000280878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280878 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 13, 37, 37, 37, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 4, 4, 4, 1, 1, 13, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1] 201 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 25, 26, 42, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280878 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 92, 201, 41, 120, 120, 36, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 120, 120, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 803 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280878 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280878 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280878/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280878 Building REAL300000280879 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280879' /scratch/stefan/7769901/working/building/REAL300000280879 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280879 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280879/0 /scratch/stefan/7769901/working/building/REAL300000280879 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1214) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1214 `/scratch/stefan/7769901/working/3D/1214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC=C2F)C=C1) `REAL300000280879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280879 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 12, 37, 37, 37, 72, 72, 72, 48, 72, 72, 72, 1, 1, 4, 4, 4, 1, 1, 72, 69, 72, 1, 1] 116 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280879 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 116, 17, 72, 72, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 116, 116, 116, 72, 72, 1, 1, 1, 72, 72] 116 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280879 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280879 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280879/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280879 Building REAL300000280880 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280880' /scratch/stefan/7769901/working/building/REAL300000280880 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280880 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280880/0 /scratch/stefan/7769901/working/building/REAL300000280880 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1215) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1215 `/scratch/stefan/7769901/working/3D/1215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1) `REAL300000280880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280880 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 40, 40, 22, 40, 40, 40, 40, 40, 40, 1, 1, 4, 4, 4, 1, 1, 9, 40, 40, 40, 1, 1] 69 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280880 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 17, 69, 12, 40, 40, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 69, 69, 69, 40, 40, 9, 1, 1, 1, 40, 40] 69 rigid atoms, others: [33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280880 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280880/1 /scratch/stefan/7769901/working/building/REAL300000280880 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1216) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1216 `/scratch/stefan/7769901/working/3D/1216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1) `REAL300000280880.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280880 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 3, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 25, 25, 25, 43, 43, 25, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 43, 43, 43, 1, 1] 65 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280880 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 18, 65, 17, 43, 43, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 65, 65, 65, 43, 43, 1, 1, 1, 43, 43] 65 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280880 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280880 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280880/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280880/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280880 Building REAL300000280881 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280881' /scratch/stefan/7769901/working/building/REAL300000280881 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280881 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280881/0 /scratch/stefan/7769901/working/building/REAL300000280881 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1217) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1217 `/scratch/stefan/7769901/working/3D/1217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2)C=C1) `REAL300000280881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280881 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 44, 44, 44, 44, 44, 44, 1, 1, 4, 4, 4, 1, 1, 44, 44, 44, 1, 1] 73 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280881 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 73, 17, 44, 44, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 44, 44, 73, 73, 73, 44, 44, 1, 1, 1, 44, 44] 73 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280881 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280881/1 /scratch/stefan/7769901/working/building/REAL300000280881 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1218) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1218 `/scratch/stefan/7769901/working/3D/1218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)N=C2)C=C1) `REAL300000280881.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280881 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 10, 43, 43, 43, 1, 1] 74 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280881 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 74, 16, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 43, 43, 74, 74, 74, 43, 43, 9, 1, 1, 1, 43, 43] 74 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280881 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280881 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280881/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280881/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280881 Building REAL300000280882 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280882' /scratch/stefan/7769901/working/building/REAL300000280882 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280882 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280882/0 /scratch/stefan/7769901/working/building/REAL300000280882 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1219) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1219 `/scratch/stefan/7769901/working/3D/1219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280882 none N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 3, 3, 3, 9, 25, 25, 9, 18, 69, 69, 69, 69, 69, 69, 25, 25, 1, 1, 1, 1, 9, 25, 25, 69, 69, 69, 25, 25, 1] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 36] 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]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280882 none N#CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25] 69 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280882 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280882/1 /scratch/stefan/7769901/working/building/REAL300000280882 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1220) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1220 `/scratch/stefan/7769901/working/3D/1220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280882.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280882 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 16, 71, 71, 71, 71, 71, 71, 27, 27, 1, 1, 1, 1, 27, 27, 71, 71, 71, 27, 27, 1] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280882 none N#CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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: [27, 27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 71 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280882 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280882 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280882/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280882/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280882 Building REAL300000280883 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280883' /scratch/stefan/7769901/working/building/REAL300000280883 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280883 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280883/0 /scratch/stefan/7769901/working/building/REAL300000280883 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1221) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1221 `/scratch/stefan/7769901/working/3D/1221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280883 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 19, 19, 13, 15, 43, 43, 43, 43, 43, 43, 19, 19, 1, 1, 1, 1, 9, 19, 19, 43, 43, 43, 19, 19, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 23, 24, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280883 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 15, 6, 1, 1, 7, 7, 7, 1, 1, 15, 15] 43 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280883 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280883/1 /scratch/stefan/7769901/working/building/REAL300000280883 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1222) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1222 `/scratch/stefan/7769901/working/3D/1222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280883.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280883 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 5, 8, 41, 41, 41, 41, 41, 41, 13, 13, 1, 1, 1, 1, 13, 13, 41, 41, 41, 13, 13, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 23, 24, 25, 26] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280883 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 13, 13, 13, 13, 1, 1, 7, 7, 7, 1, 1, 13, 13] 41 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280883 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280883 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280883/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280883/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280883 Building REAL300000280884 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280884' /scratch/stefan/7769901/working/building/REAL300000280884 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280884 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280884/0 /scratch/stefan/7769901/working/building/REAL300000280884 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1223) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1223 `/scratch/stefan/7769901/working/3D/1223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2F)C=C1) `REAL300000280884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280884 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 85, 85, 31, 74, 85, 85, 85, 1, 1, 4, 4, 4, 1, 1, 85, 85, 85, 1, 1] 127 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280884 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 127, 45, 85, 85, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 127, 127, 127, 85, 85, 1, 1, 1, 85, 85] 127 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280884 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280884 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280884/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280884 Building REAL300000280885 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280885' /scratch/stefan/7769901/working/building/REAL300000280885 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280885 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280885/0 /scratch/stefan/7769901/working/building/REAL300000280885 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1224) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1224 `/scratch/stefan/7769901/working/3D/1224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280885 none N#CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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, 1, 7, 7, 7, 15, 29, 29, 16, 20, 81, 81, 81, 81, 81, 81, 29, 29, 1, 1, 1, 1, 29, 29, 81, 81, 81, 29, 29] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280885 none N#CC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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: [29, 29, 29, 29, 23, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 29, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1] 81 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280885 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280885/1 /scratch/stefan/7769901/working/building/REAL300000280885 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1225) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1225 `/scratch/stefan/7769901/working/3D/1225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280885.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280885 none N#CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 23, 23, 17, 19, 61, 61, 61, 61, 61, 61, 23, 23, 1, 1, 1, 1, 11, 23, 23, 61, 61, 61, 23, 23] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280885 none N#CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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: [23, 23, 23, 23, 19, 23, 23, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 23, 23, 6, 1, 1, 7, 7, 7, 1, 1] 61 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280885 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280885 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280885/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280885/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280885 Building REAL300000280886 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280886' /scratch/stefan/7769901/working/building/REAL300000280886 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280886 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280886/0 /scratch/stefan/7769901/working/building/REAL300000280886 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1226) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1226 `/scratch/stefan/7769901/working/3D/1226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280886 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 24, 24, 24, 26, 26, 26, 26, 26, 26, 34, 34, 26, 1, 1, 4, 4, 4, 1, 1, 9, 26, 26, 26, 1, 1] 59 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280886 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 59, 7, 26, 26, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 26, 59, 59, 59, 26, 26, 7, 1, 1, 1, 26, 26] 59 rigid atoms, others: [33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280886 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280886/1 /scratch/stefan/7769901/working/building/REAL300000280886 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1227) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1227 `/scratch/stefan/7769901/working/3D/1227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000280886.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280886 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 29, 29, 29, 29, 29, 29, 37, 37, 29, 1, 1, 4, 4, 4, 1, 1, 29, 29, 29, 1, 1] 65 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280886 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 11, 65, 11, 29, 29, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 65, 65, 65, 29, 29, 1, 1, 1, 29, 29] 65 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280886 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280886 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280886/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280886/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280886 Building REAL300000280887 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280887' /scratch/stefan/7769901/working/building/REAL300000280887 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280887 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280887/0 /scratch/stefan/7769901/working/building/REAL300000280887 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1228) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1228 `/scratch/stefan/7769901/working/3D/1228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-]) `REAL300000280887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280887 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 9, 16, 65, 65, 65, 65, 65, 65, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 23, 23, 65, 65, 65, 23, 23, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280887 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 1, 1, 7, 7, 7, 1, 1, 23] 65 rigid atoms, others: [33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280887 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280887/1 /scratch/stefan/7769901/working/building/REAL300000280887 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1229) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1229 `/scratch/stefan/7769901/working/3D/1229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-]) `REAL300000280887.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280887 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 27, 27, 9, 16, 67, 67, 67, 67, 67, 67, 27, 27, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 27, 27, 67, 67, 67, 27, 27, 1] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280887 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 67 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280887 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280887 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280887/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280887/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280887 Building REAL300000280888 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280888' /scratch/stefan/7769901/working/building/REAL300000280888 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280888 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280888/0 /scratch/stefan/7769901/working/building/REAL300000280888 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1230) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1230 `/scratch/stefan/7769901/working/3D/1230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280888 none CC1=NNC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 36, 36, 19, 24, 95, 95, 95, 95, 95, 95, 36, 36, 2, 2, 2, 1, 2, 2, 2, 36, 36, 95, 95, 95, 36, 36] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280888 none CC1=NNC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 28, 28, 28, 28, 28, 28, 28, 1, 1, 7, 7, 7, 1, 1] 75 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280888 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280888 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280888/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280888 Building REAL300000280889 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280889' /scratch/stefan/7769901/working/building/REAL300000280889 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280889 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280889/0 /scratch/stefan/7769901/working/building/REAL300000280889 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1231) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1231 `/scratch/stefan/7769901/working/3D/1231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1) `REAL300000280889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280889 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1] 71 rigid atoms, others: [5, 7, 8, 9, 10, 11, 44, 45, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280889 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 18, 71, 15, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 71, 71, 71, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 71 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280889 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280889/1 /scratch/stefan/7769901/working/building/REAL300000280889 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1232) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1232 `/scratch/stefan/7769901/working/3D/1232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1) `REAL300000280889.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280889 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 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] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 4, 4, 4, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1] 72 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 44, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280889 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 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] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 72, 9, 44, 44, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 72, 72, 72, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44] 72 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 43, 44]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280889 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280889 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280889/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280889/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280889 Building REAL300000280890 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280890' /scratch/stefan/7769901/working/building/REAL300000280890 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280890 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280890/0 /scratch/stefan/7769901/working/building/REAL300000280890 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1233) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1233 `/scratch/stefan/7769901/working/3D/1233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000280890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280890 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 4, 4, 4, 1, 1, 9, 22, 22, 22, 22, 1, 1] 35 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280890 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 35, 5, 22, 22, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 35, 35, 35, 22, 22, 5, 1, 1, 1, 1, 22, 22] 35 rigid atoms, others: [32, 33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280890 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280890/1 /scratch/stefan/7769901/working/building/REAL300000280890 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1234) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1234 `/scratch/stefan/7769901/working/3D/1234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000280890.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280890 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 4, 4, 4, 1, 1, 22, 22, 22, 22, 1, 1] 35 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280890 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 35, 5, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 35, 35, 35, 22, 22, 1, 1, 1, 1, 22, 22] 35 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280890 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280890 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280890/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280890/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280890 Building REAL300000280891 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280891' /scratch/stefan/7769901/working/building/REAL300000280891 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280891 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280891/0 /scratch/stefan/7769901/working/building/REAL300000280891 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1235) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1235 `/scratch/stefan/7769901/working/3D/1235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280891 none COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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: [2, 1, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 23, 47, 47, 23, 33, 155, 155, 155, 155, 201, 201, 47, 47, 1, 3, 3, 3, 1, 1, 4, 4, 4, 47, 47, 155, 155, 155, 47, 47, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 42, 26, 30, 31] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280891 none COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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: [65, 47, 47, 47, 47, 47, 47, 71, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 47, 65, 65, 65, 47, 47, 71, 71, 71, 1, 1, 7, 7, 7, 1, 1, 47] 201 rigid atoms, others: [35, 36, 40, 41, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280891 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280891 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280891/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280891 Building REAL300000280892 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280892' /scratch/stefan/7769901/working/building/REAL300000280892 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280892 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280892/0 /scratch/stefan/7769901/working/building/REAL300000280892 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1236) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1236 `/scratch/stefan/7769901/working/3D/1236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC) `REAL300000280892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280892 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 15, 87, 87, 87, 87, 147, 147, 21, 21, 1, 1, 1, 3, 4, 4, 4, 1, 1, 9, 21, 21, 87, 87, 87, 21, 21, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 23, 24, 25, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280892 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 21, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 21, 21, 21, 55, 55, 55, 55, 21, 21, 4, 1, 1, 7, 7, 7, 1, 1, 21, 55, 55, 55] 201 rigid atoms, others: [33, 34, 38, 39, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280892 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280892/1 /scratch/stefan/7769901/working/building/REAL300000280892 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1237) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1237 `/scratch/stefan/7769901/working/3D/1237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC) `REAL300000280892.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280892 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 9, 15, 92, 92, 92, 92, 156, 156, 23, 23, 1, 1, 1, 3, 4, 4, 4, 1, 1, 23, 23, 92, 92, 92, 23, 23, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 23, 24, 25, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280892 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 23, 23, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 23, 23, 23, 57, 59, 59, 59, 23, 23, 1, 1, 7, 7, 7, 1, 1, 23, 57, 57, 57] 201 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280892 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280892 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280892/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280892/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280892 Building REAL300000280893 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280893' /scratch/stefan/7769901/working/building/REAL300000280893 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280893 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280893/0 /scratch/stefan/7769901/working/building/REAL300000280893 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1238) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1238 `/scratch/stefan/7769901/working/3D/1238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCC3=C2)C=C1) `REAL300000280893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280893 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 23, 23, 23, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1] 75 rigid atoms, others: [5, 7, 8, 9, 10, 11, 42, 41, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280893 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3CCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 75, 19, 75, 9, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 75, 75, 75, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 75 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280893 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280893/1 /scratch/stefan/7769901/working/building/REAL300000280893 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1239) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1239 `/scratch/stefan/7769901/working/3D/1239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCC3=C2)C=C1) `REAL300000280893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280893 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 4, 4, 4, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1] 75 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280893 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3CCCC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 75, 18, 75, 9, 45, 45, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 75, 75, 75, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 75 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 40, 41]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280893 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280893 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280893/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280893/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280893 Building REAL300000280894 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280894' /scratch/stefan/7769901/working/building/REAL300000280894 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280894 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280894/0 /scratch/stefan/7769901/working/building/REAL300000280894 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1240) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1240 `/scratch/stefan/7769901/working/3D/1240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280894 none CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 63, 63, 34, 41, 168, 168, 168, 168, 168, 168, 63, 63, 2, 2, 2, 2, 2, 2, 63, 63, 168, 168, 168, 63, 63] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280894 none CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 63, 63, 63, 63, 63, 63, 1, 1, 7, 7, 7, 1, 1] 168 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280894 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280894 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280894/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280894 Building REAL300000280895 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280895' /scratch/stefan/7769901/working/building/REAL300000280895 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280895 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280895/0 /scratch/stefan/7769901/working/building/REAL300000280895 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1241) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1241 `/scratch/stefan/7769901/working/3D/1241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000280895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280895 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 1, 1] 41 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280895 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 11, 41, 7, 21, 21, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 41, 41, 41, 21, 21, 7, 1, 1, 1, 1, 21, 21] 41 rigid atoms, others: [32, 33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280895 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280895/1 /scratch/stefan/7769901/working/building/REAL300000280895 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1242) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1242 `/scratch/stefan/7769901/working/3D/1242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000280895.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280895 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 1, 1, 21, 21, 21, 21, 1, 1] 39 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280895 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 39, 11, 21, 21, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 39, 39, 39, 21, 21, 1, 1, 1, 1, 21, 21] 39 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280895 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280895 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280895/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280895/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280895 Building REAL300000280896 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280896' /scratch/stefan/7769901/working/building/REAL300000280896 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280896 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280896/0 /scratch/stefan/7769901/working/building/REAL300000280896 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1243) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1243 `/scratch/stefan/7769901/working/3D/1243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1) `REAL300000280896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280896 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 10, 43, 43, 43, 1, 1] 74 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280896 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 74, 15, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 74, 74, 74, 43, 43, 9, 1, 1, 1, 43, 43] 74 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280896 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280896/1 /scratch/stefan/7769901/working/building/REAL300000280896 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1244) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1244 `/scratch/stefan/7769901/working/3D/1244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1) `REAL300000280896.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280896 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 43, 43, 43, 1, 1] 69 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280896 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 18, 69, 14, 43, 43, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 69, 69, 69, 43, 43, 1, 1, 1, 43, 43] 69 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280896 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280896 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280896/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280896/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280896 Building REAL300000280897 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280897' /scratch/stefan/7769901/working/building/REAL300000280897 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280897 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280897/0 /scratch/stefan/7769901/working/building/REAL300000280897 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1245) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1245 `/scratch/stefan/7769901/working/3D/1245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280897 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 9, 21, 78, 78, 78, 78, 78, 78, 29, 29, 1, 2, 2, 2, 1, 1, 1, 9, 29, 29, 78, 78, 78, 29, 29, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 23, 27, 28, 29] set([7, 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]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280897 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 7, 7, 7, 1, 1, 29] 78 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280897 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280897/1 /scratch/stefan/7769901/working/building/REAL300000280897 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1246) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1246 `/scratch/stefan/7769901/working/3D/1246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280897.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280897 none CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 15, 17, 76, 76, 76, 76, 76, 76, 27, 27, 1, 2, 2, 2, 1, 1, 1, 27, 27, 76, 76, 76, 27, 27, 1] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 27, 28, 29, 37] set([7, 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]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280897 none CC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 76 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280897 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280897 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280897/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280897/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280897 Building REAL300000280898 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280898' /scratch/stefan/7769901/working/building/REAL300000280898 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280898 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280898/0 /scratch/stefan/7769901/working/building/REAL300000280898 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1247) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1247 `/scratch/stefan/7769901/working/3D/1247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2)C=C1) `REAL300000280898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280898 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 21, 21, 21, 95, 95, 159, 159, 140, 159, 159, 1, 1, 3, 3, 3, 1, 1, 7, 95, 95, 159, 159, 140, 159, 159, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 23, 24, 39, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280898 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C=CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 131, 201, 117, 159, 159, 86, 45, 6, 45, 45, 6, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 159, 159, 86, 6, 6, 1, 1, 1, 1, 1, 159, 159] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39]) total number of confs: 733 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280898 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280898 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280898/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280898 Building REAL300000280899 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280899' /scratch/stefan/7769901/working/building/REAL300000280899 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280899 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280899/0 /scratch/stefan/7769901/working/building/REAL300000280899 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1248) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1248 `/scratch/stefan/7769901/working/3D/1248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2)C=C1) `REAL300000280899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280899 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 11, 41, 41, 41, 41, 1, 1] 73 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280899 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 73, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 41, 41, 73, 73, 73, 41, 41, 9, 1, 1, 1, 1, 41, 41] 73 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280899 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280899/1 /scratch/stefan/7769901/working/building/REAL300000280899 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1249) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1249 `/scratch/stefan/7769901/working/3D/1249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2)C=C1) `REAL300000280899.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280899 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 24, 24, 24, 40, 40, 40, 40, 40, 40, 1, 1, 4, 4, 4, 1, 1, 40, 40, 40, 40, 1, 1] 72 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280899 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 72, 16, 40, 40, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 40, 40, 72, 72, 72, 40, 40, 1, 1, 1, 1, 40, 40] 72 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280899 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280899 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280899/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280899/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280899 Building REAL300000280900 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280900' /scratch/stefan/7769901/working/building/REAL300000280900 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280900 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280900/0 /scratch/stefan/7769901/working/building/REAL300000280900 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1250) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1250 `/scratch/stefan/7769901/working/3D/1250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280900 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 9, 18, 99, 99, 99, 99, 136, 136, 25, 25, 1, 1, 6, 6, 6, 1, 1, 9, 25, 25, 99, 99, 99, 25, 25, 1, 1] 136 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 24, 25, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 454 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280900 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [71, 25, 71, 15, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 71, 71, 71, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25, 25] 136 rigid atoms, others: [32, 33, 37, 38, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40]) total number of confs: 295 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280900 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280900/1 /scratch/stefan/7769901/working/building/REAL300000280900 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1251) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1251 `/scratch/stefan/7769901/working/3D/1251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280900 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 16, 104, 104, 104, 104, 136, 136, 27, 27, 1, 1, 6, 6, 6, 1, 1, 27, 27, 104, 104, 104, 27, 27, 1, 1] 140 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 24, 25, 38, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280900 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 27, 69, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 69, 69, 69, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27, 27] 140 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280900 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280900 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280900/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280900/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280900 Building REAL300000280901 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280901' /scratch/stefan/7769901/working/building/REAL300000280901 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280901 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280901/0 /scratch/stefan/7769901/working/building/REAL300000280901 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1252) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1252 `/scratch/stefan/7769901/working/3D/1252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280901 none CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 13, 45, 45, 45, 45, 45, 45, 17, 17, 1, 2, 2, 2, 1, 1, 2, 2, 2, 5, 17, 17, 45, 45, 45, 17, 17, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 24, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280901 none CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 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, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 7, 7, 7, 1, 1, 17] 45 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280901 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280901/1 /scratch/stefan/7769901/working/building/REAL300000280901 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1253) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1253 `/scratch/stefan/7769901/working/3D/1253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280901.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280901 none CC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 9, 49, 49, 49, 49, 49, 49, 17, 17, 1, 2, 2, 2, 1, 1, 2, 2, 2, 17, 17, 49, 49, 49, 17, 17, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 24, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280901 none CC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 7, 7, 7, 1, 1, 17] 49 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280901 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280901 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280901/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280901/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280901 Building REAL300000280902 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280902' /scratch/stefan/7769901/working/building/REAL300000280902 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280902 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280902/0 /scratch/stefan/7769901/working/building/REAL300000280902 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1254) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1254 `/scratch/stefan/7769901/working/3D/1254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280902 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 9, 21, 80, 80, 80, 80, 80, 80, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 9, 29, 29, 80, 80, 80, 29, 29, 1, 2, 2, 2] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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, 39, 40, 41]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280902 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 7, 7, 7, 1, 1, 29, 29, 29, 29] 80 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280902 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280902/1 /scratch/stefan/7769901/working/building/REAL300000280902 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1255) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1255 `/scratch/stefan/7769901/working/3D/1255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280902.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280902 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 27, 27, 10, 16, 77, 77, 77, 77, 77, 77, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 77, 77, 77, 27, 27, 1, 2, 2, 2] 77 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: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280902 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27, 27, 27, 27] 77 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280902 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280902 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280902/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280902/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280902 Building REAL300000280903 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280903' /scratch/stefan/7769901/working/building/REAL300000280903 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280903 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280903/0 /scratch/stefan/7769901/working/building/REAL300000280903 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1256) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1256 `/scratch/stefan/7769901/working/3D/1256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1) `REAL300000280903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280903 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 10, 43, 43, 43, 1, 1] 75 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280903 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 75, 17, 75, 16, 43, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 75, 75, 75, 43, 43, 9, 1, 1, 1, 43, 43] 75 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280903 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280903/1 /scratch/stefan/7769901/working/building/REAL300000280903 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1257) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1257 `/scratch/stefan/7769901/working/3D/1257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1) `REAL300000280903.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280903 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 45, 45, 45, 45, 45, 45, 45, 1, 1, 4, 4, 4, 1, 1, 45, 45, 45, 1, 1] 70 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280903 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 70, 13, 45, 45, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 70, 70, 70, 45, 45, 1, 1, 1, 45, 45] 70 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280903 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280903 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280903/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280903/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280903 Building REAL300000280904 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280904' /scratch/stefan/7769901/working/building/REAL300000280904 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280904 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280904/0 /scratch/stefan/7769901/working/building/REAL300000280904 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1258) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1258 `/scratch/stefan/7769901/working/3D/1258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280904 none CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 10, 13, 68, 68, 68, 68, 121, 121, 17, 17, 1, 11, 11, 11, 1, 1, 1, 9, 17, 17, 68, 68, 68, 17, 17, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 40, 25, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280904 none CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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: [101, 17, 101, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 1, 1, 17, 101, 101, 101, 17, 17, 17, 4, 1, 1, 6, 6, 6, 1, 1, 17] 201 rigid atoms, others: [33, 34, 38, 39, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280904 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280904/1 /scratch/stefan/7769901/working/building/REAL300000280904 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1259) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1259 `/scratch/stefan/7769901/working/3D/1259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280904.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280904 none CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 15, 15, 89, 89, 89, 89, 135, 135, 25, 25, 1, 12, 12, 12, 1, 1, 1, 25, 25, 89, 89, 89, 25, 25, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 39, 25, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 456 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280904 none CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 96, 25, 25, 25, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 25, 96, 96, 96, 25, 25, 25, 1, 1, 7, 7, 7, 1, 1, 25] 201 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 287 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280904 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280904 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280904/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280904/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280904 Building REAL300000280905 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280905' /scratch/stefan/7769901/working/building/REAL300000280905 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280905 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280905/0 /scratch/stefan/7769901/working/building/REAL300000280905 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1260) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1260 `/scratch/stefan/7769901/working/3D/1260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280905 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 13, 27, 27, 13, 22, 69, 69, 69, 69, 69, 69, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 13, 27, 27, 69, 69, 69, 27, 27, 2, 2, 2, 1] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 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]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280905 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 7, 7, 7, 1, 1, 27, 27, 27, 27] 69 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280905 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280905/1 /scratch/stefan/7769901/working/building/REAL300000280905 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1261) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1261 `/scratch/stefan/7769901/working/3D/1261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280905.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280905 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 35, 35, 20, 25, 93, 93, 93, 93, 93, 93, 35, 35, 1, 1, 1, 2, 2, 2, 1, 1, 35, 35, 93, 93, 93, 35, 35, 2, 2, 2, 1] 93 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]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280905 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 19, 35, 35, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 7, 7, 7, 1, 1, 35, 35, 35, 35] 93 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280905 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280905 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280905/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280905/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280905 Building REAL300000280906 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280906' /scratch/stefan/7769901/working/building/REAL300000280906 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280906 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280906/0 /scratch/stefan/7769901/working/building/REAL300000280906 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1262) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1262 `/scratch/stefan/7769901/working/3D/1262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280906 none COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 43, 43, 17, 28, 119, 119, 119, 119, 120, 120, 43, 43, 7, 7, 7, 1, 1, 1, 1, 43, 43, 119, 119, 119, 43, 43] 183 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 3, 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: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280906 none COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 43, 81, 43, 43, 25, 43, 43, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 81, 81, 81, 43, 43, 43, 43, 1, 1, 7, 7, 7, 1, 1] 183 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280906 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280906 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280906/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280906 Building REAL300000280907 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280907' /scratch/stefan/7769901/working/building/REAL300000280907 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280907 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280907/0 /scratch/stefan/7769901/working/building/REAL300000280907 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1263) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1263 `/scratch/stefan/7769901/working/3D/1263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280907 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 20, 9, 16, 52, 52, 52, 52, 88, 88, 20, 20, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 20, 20, 52, 52, 52, 20, 20, 1, 1] 88 rigid atoms, others: [1, 4, 5, 6, 7, 8, 46, 47, 25, 36, 26, 37] set([0, 2, 3, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280907 none CC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 34, 34, 20, 20, 20, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 6, 1, 1, 7, 7, 7, 1, 1, 20, 20] 88 rigid atoms, others: [45, 39, 40, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280907 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280907/1 /scratch/stefan/7769901/working/building/REAL300000280907 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1264) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1264 `/scratch/stefan/7769901/working/3D/1264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280907.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280907 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 9, 14, 58, 58, 58, 58, 87, 87, 20, 20, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 20, 20, 58, 58, 58, 20, 20, 1, 1] 87 rigid atoms, others: [1, 4, 5, 6, 7, 8, 45, 46, 25, 36, 26, 37] set([0, 2, 3, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280907 none CC(C)(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 37, 37, 20, 20, 20, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 1, 1, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 20, 1, 1, 7, 7, 7, 1, 1, 20, 20] 87 rigid atoms, others: [43, 38, 39, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280907 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280907 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280907/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280907/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280907 Building REAL300000280908 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280908' /scratch/stefan/7769901/working/building/REAL300000280908 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280908 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280908/0 /scratch/stefan/7769901/working/building/REAL300000280908 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1265) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1265 `/scratch/stefan/7769901/working/3D/1265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280908 none CC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 20, 9, 18, 73, 73, 73, 73, 74, 74, 20, 20, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 9, 20, 20, 73, 73, 73, 20, 20, 1, 1] 81 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 7, 44, 43, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280908 none CC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 20, 23, 20, 20, 20, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 20, 20, 23, 23, 23, 23, 23, 23, 23, 20, 20, 6, 1, 1, 7, 7, 7, 1, 1, 20, 20] 81 rigid atoms, others: [36, 37, 41, 10, 11, 12, 13, 14, 15, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280908 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280908/1 /scratch/stefan/7769901/working/building/REAL300000280908 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1266) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1266 `/scratch/stefan/7769901/working/3D/1266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280908.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280908 none CC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 2, 2, 2, 9, 22, 22, 9, 14, 71, 71, 71, 71, 73, 73, 22, 22, 1, 1, 3, 3, 3, 2, 3, 3, 3, 1, 1, 22, 22, 71, 71, 71, 22, 22, 1, 1] 81 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 42, 7, 43, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280908 none CC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 22, 28, 22, 22, 22, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 22, 22, 28, 28, 28, 28, 28, 28, 28, 22, 22, 1, 1, 7, 7, 7, 1, 1, 22, 22] 81 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280908 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280908 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280908/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280908/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280908 Building REAL300000280909 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280909' /scratch/stefan/7769901/working/building/REAL300000280909 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280909 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280909/0 /scratch/stefan/7769901/working/building/REAL300000280909 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1267) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1267 `/scratch/stefan/7769901/working/3D/1267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280909 none CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [9, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 10, 20, 92, 92, 92, 92, 155, 155, 28, 28, 1, 1, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 9, 28, 28, 92, 92, 92, 28, 28, 1, 1] 189 rigid atoms, others: [2, 36, 5, 6, 7, 8, 46, 47, 25, 4, 26, 37] set([0, 1, 3, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280909 none CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [79, 54, 28, 54, 28, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 28, 28, 79, 79, 79, 79, 79, 54, 54, 54, 54, 28, 28, 6, 1, 1, 7, 7, 7, 1, 1, 28, 28] 189 rigid atoms, others: [45, 39, 40, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280909 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280909/1 /scratch/stefan/7769901/working/building/REAL300000280909 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1268) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1268 `/scratch/stefan/7769901/working/3D/1268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280909.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280909 none CCC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 15, 16, 94, 94, 94, 94, 158, 158, 25, 25, 1, 1, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 25, 25, 94, 94, 94, 25, 25, 1, 1] 201 rigid atoms, others: [2, 36, 5, 6, 7, 8, 45, 46, 25, 4, 26, 37] set([0, 1, 3, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280909 none CCC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 25, 61, 25, 25, 25, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 25, 25, 89, 89, 89, 89, 89, 61, 61, 61, 61, 25, 25, 1, 1, 7, 7, 7, 1, 1, 25, 25] 201 rigid atoms, others: [43, 38, 39, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280909 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280909 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280909/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280909/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280909 Building REAL300000280910 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280910' /scratch/stefan/7769901/working/building/REAL300000280910 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280910 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280910/0 /scratch/stefan/7769901/working/building/REAL300000280910 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1269) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1269 `/scratch/stefan/7769901/working/3D/1269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)S2)C=C1) `REAL300000280910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280910 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 74, 74, 74, 74, 74, 1, 1, 4, 4, 4, 1, 1, 74, 74, 1, 1] 119 rigid atoms, others: [5, 7, 8, 9, 10, 11, 21, 22, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280910 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 53, 119, 33, 74, 74, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 74, 74, 119, 119, 119, 74, 74, 1, 1, 74, 74] 119 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280910 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280910 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280910/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280910 Building REAL300000280911 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280911' /scratch/stefan/7769901/working/building/REAL300000280911 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280911 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280911/0 /scratch/stefan/7769901/working/building/REAL300000280911 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1270) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1270 `/scratch/stefan/7769901/working/3D/1270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280911 none CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 9, 21, 93, 93, 93, 93, 146, 146, 29, 29, 1, 1, 9, 9, 9, 9, 9, 5, 5, 1, 1, 9, 29, 29, 93, 93, 93, 29, 29, 1, 1] 200 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 24, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280911 none CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 56, 15, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 85, 85, 85, 85, 85, 56, 56, 29, 29, 6, 1, 1, 7, 7, 7, 1, 1, 29, 29] 200 rigid atoms, others: [36, 37, 41, 10, 11, 12, 13, 14, 15, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280911 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280911/1 /scratch/stefan/7769901/working/building/REAL300000280911 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1271) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1271 `/scratch/stefan/7769901/working/3D/1271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280911.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280911 none CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 9, 16, 94, 94, 94, 94, 147, 147, 28, 28, 1, 1, 8, 8, 8, 8, 8, 4, 4, 1, 1, 28, 28, 94, 94, 94, 28, 28, 1, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 24, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280911 none CCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 15, 15, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 28, 28, 93, 93, 93, 93, 93, 59, 59, 28, 28, 1, 1, 7, 7, 7, 1, 1, 28, 28] 201 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280911 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280911 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280911/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280911/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280911 Building REAL300000280912 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280912' /scratch/stefan/7769901/working/building/REAL300000280912 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280912 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280912/0 /scratch/stefan/7769901/working/building/REAL300000280912 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1272) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1272 `/scratch/stefan/7769901/working/3D/1272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280912 none COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 33, 38, 160, 160, 160, 160, 172, 172, 49, 49, 4, 4, 4, 1, 1, 1, 1, 49, 49, 160, 160, 160, 49, 49] 172 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280912 none COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 49, 49, 27, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 69, 69, 69, 49, 49, 49, 49, 1, 1, 7, 7, 7, 1, 1] 172 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280912 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280912/1 /scratch/stefan/7769901/working/building/REAL300000280912 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1273) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1273 `/scratch/stefan/7769901/working/3D/1273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280912.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280912 none COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 51, 51, 25, 38, 146, 146, 146, 146, 146, 146, 51, 51, 4, 4, 4, 1, 1, 1, 1, 25, 51, 51, 146, 146, 146, 51, 51] 146 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 480 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280912 none COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [61, 51, 51, 51, 27, 51, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 61, 61, 61, 51, 51, 51, 51, 6, 1, 1, 7, 7, 7, 1, 1] 146 rigid atoms, others: [33, 34, 38, 39, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 259 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280912 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280912 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280912/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280912/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280912 Building REAL300000280913 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280913' /scratch/stefan/7769901/working/building/REAL300000280913 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280913 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280913/0 /scratch/stefan/7769901/working/building/REAL300000280913 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1274) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1274 `/scratch/stefan/7769901/working/3D/1274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-]) `REAL300000280913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280913 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 16, 16, 7, 12, 60, 60, 60, 60, 60, 60, 16, 16, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 16, 16, 60, 60, 60, 16, 16, 1] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280913 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 16, 16, 16, 22, 22, 16, 16, 16, 16, 16, 5, 1, 1, 7, 7, 7, 1, 1, 16] 60 rigid atoms, others: [33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280913 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280913/1 /scratch/stefan/7769901/working/building/REAL300000280913 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1275) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1275 `/scratch/stefan/7769901/working/3D/1275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-]) `REAL300000280913.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280913 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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, 2, 2, 2, 7, 17, 17, 7, 11, 59, 59, 59, 59, 59, 59, 17, 17, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 17, 17, 59, 59, 59, 17, 17, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280913 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 17, 17, 17, 23, 23, 17, 17, 17, 17, 17, 1, 1, 7, 7, 7, 1, 1, 17] 59 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280913 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280913 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280913/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280913/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280913 Building REAL300000280914 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280914' /scratch/stefan/7769901/working/building/REAL300000280914 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280914 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280914/0 /scratch/stefan/7769901/working/building/REAL300000280914 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1276) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1276 `/scratch/stefan/7769901/working/3D/1276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2F)C=C1) `REAL300000280914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280914 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 33, 33, 33, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 4, 4, 4, 1, 1, 86, 86, 1, 1] 142 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280914 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 142, 25, 86, 86, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 142, 142, 142, 86, 86, 1, 1, 86, 86] 142 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280914 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280914 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280914/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280914 Building REAL300000280915 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280915' /scratch/stefan/7769901/working/building/REAL300000280915 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280915 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280915/0 /scratch/stefan/7769901/working/building/REAL300000280915 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1277) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1277 `/scratch/stefan/7769901/working/3D/1277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2Cl)C=C1) `REAL300000280915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280915 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 39, 39, 31, 39, 39, 39, 1, 1, 4, 4, 4, 1, 1, 39, 39, 35, 39, 1, 1] 63 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280915 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 63, 20, 39, 39, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 39, 39, 63, 63, 63, 39, 39, 1, 1, 1, 1, 39, 39] 63 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280915 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280915/1 /scratch/stefan/7769901/working/building/REAL300000280915 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1278) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1278 `/scratch/stefan/7769901/working/3D/1278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2Cl)C=C1) `REAL300000280915.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280915 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 28, 28, 28, 36, 36, 32, 36, 36, 36, 1, 1, 4, 4, 4, 1, 1, 11, 36, 36, 32, 36, 1, 1] 56 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280915 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 56, 14, 36, 36, 10, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 36, 36, 56, 56, 56, 36, 36, 10, 1, 1, 1, 1, 36, 36] 56 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280915 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280915 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280915/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280915/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280915 Building REAL300000280916 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280916' /scratch/stefan/7769901/working/building/REAL300000280916 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280916 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280916/0 /scratch/stefan/7769901/working/building/REAL300000280916 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1279) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1279 `/scratch/stefan/7769901/working/3D/1279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280916 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 4, 4, 4, 1, 1, 43, 43, 43, 43, 1, 1] 67 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280916 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 19, 67, 9, 43, 43, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 67, 67, 67, 43, 43, 1, 1, 1, 1, 43, 43] 67 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280916 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280916/1 /scratch/stefan/7769901/working/building/REAL300000280916 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1280) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1280 `/scratch/stefan/7769901/working/3D/1280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000280916.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280916 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 4, 4, 4, 1, 1, 9, 38, 38, 38, 38, 1, 1] 66 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280916 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 17, 66, 10, 38, 38, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 66, 66, 66, 38, 38, 9, 1, 1, 1, 1, 38, 38] 66 rigid atoms, others: [32, 33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280916 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280916 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280916/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280916/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280916 Building REAL300000280917 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280917' /scratch/stefan/7769901/working/building/REAL300000280917 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280917 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280917/0 /scratch/stefan/7769901/working/building/REAL300000280917 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1281) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1281 `/scratch/stefan/7769901/working/3D/1281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280917 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 33, 33, 19, 24, 90, 90, 90, 90, 90, 90, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 90, 90, 90, 33, 33] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280917 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 25, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 33, 33, 33, 33, 27, 33, 1, 1, 7, 7, 7, 1, 1] 90 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280917 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280917/1 /scratch/stefan/7769901/working/building/REAL300000280917 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1282) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1282 `/scratch/stefan/7769901/working/3D/1282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280917.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280917 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 13, 23, 82, 82, 82, 82, 82, 82, 29, 29, 2, 2, 2, 1, 1, 1, 13, 29, 29, 82, 82, 82, 29, 29] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280917 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 21, 29, 29, 29, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 29, 29, 21, 29, 6, 1, 1, 7, 7, 7, 1, 1] 82 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280917 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280917 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280917/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280917/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280917 Building REAL300000280918 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280918' /scratch/stefan/7769901/working/building/REAL300000280918 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280918 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280918/0 /scratch/stefan/7769901/working/building/REAL300000280918 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1283) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1283 `/scratch/stefan/7769901/working/3D/1283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1) `REAL300000280918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280918 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 72, 72, 72, 72, 1, 1, 4, 4, 4, 1, 1, 72, 72, 72, 1, 1] 125 rigid atoms, others: [5, 7, 8, 9, 10, 11, 20, 21, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280918 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 50, 125, 38, 72, 72, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 72, 72, 125, 125, 125, 72, 72, 1, 1, 1, 72, 72] 125 rigid atoms, others: [12, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280918 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280918 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280918/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280918 Building REAL300000280919 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280919' /scratch/stefan/7769901/working/building/REAL300000280919 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280919 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280919/0 /scratch/stefan/7769901/working/building/REAL300000280919 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1284) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1284 `/scratch/stefan/7769901/working/3D/1284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280919 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 16, 18, 74, 74, 74, 74, 74, 74, 25, 25, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 74, 74, 74, 25, 25, 1, 1] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280919 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25, 25] 74 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280919 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280919/1 /scratch/stefan/7769901/working/building/REAL300000280919 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1285) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1285 `/scratch/stefan/7769901/working/3D/1285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280919.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280919 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 29, 29, 9, 15, 89, 89, 89, 89, 89, 89, 29, 29, 1, 1, 2, 2, 2, 1, 1, 29, 29, 89, 89, 89, 29, 29, 1, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 38, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280919 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1, 29, 29] 89 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280919 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280919 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280919/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280919/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280919 Building REAL300000280920 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280920' /scratch/stefan/7769901/working/building/REAL300000280920 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280920 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280920/0 /scratch/stefan/7769901/working/building/REAL300000280920 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1286) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1286 `/scratch/stefan/7769901/working/3D/1286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])C=C1) `REAL300000280920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280920 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 4, 1, 1, 26, 26, 26, 26, 1, 1] 43 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280920 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 43, 5, 26, 26, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 26, 26, 43, 43, 43, 26, 26, 1, 1, 1, 1, 26, 26] 43 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280920 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280920 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280920/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280920 Building REAL300000280921 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280921' /scratch/stefan/7769901/working/building/REAL300000280921 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280921 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280921/0 /scratch/stefan/7769901/working/building/REAL300000280921 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1287) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1287 `/scratch/stefan/7769901/working/3D/1287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280921 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 9, 13, 41, 41, 41, 41, 41, 41, 16, 16, 1, 1, 2, 2, 2, 1, 1, 9, 16, 16, 41, 41, 41, 16, 16, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280921 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 7, 7, 7, 1, 1, 15, 15] 41 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280921 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280921/1 /scratch/stefan/7769901/working/building/REAL300000280921 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1288) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1288 `/scratch/stefan/7769901/working/3D/1288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280921.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280921 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 15, 15, 5, 9, 42, 42, 42, 42, 42, 42, 15, 15, 1, 1, 2, 2, 2, 1, 1, 15, 15, 42, 42, 42, 15, 15, 1, 1] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 36, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280921 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 7, 7, 7, 1, 1, 15, 15] 42 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280921 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280921 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280921/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280921/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280921 Building REAL300000280922 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280922' /scratch/stefan/7769901/working/building/REAL300000280922 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280922 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280922/0 /scratch/stefan/7769901/working/building/REAL300000280922 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1289) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1289 `/scratch/stefan/7769901/working/3D/1289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280922 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [12, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 15, 87, 87, 87, 87, 149, 149, 21, 21, 1, 1, 12, 12, 12, 12, 12, 1, 1, 9, 21, 21, 87, 87, 87, 21, 21, 1, 1] 160 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 42, 24, 25, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 540 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280922 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [68, 44, 11, 11, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 21, 21, 68, 68, 68, 68, 68, 21, 21, 4, 1, 1, 7, 7, 7, 1, 1, 21, 21] 160 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42]) total number of confs: 297 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280922 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280922/1 /scratch/stefan/7769901/working/building/REAL300000280922 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1290) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1290 `/scratch/stefan/7769901/working/3D/1290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280922.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280922 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 9, 15, 97, 97, 97, 97, 163, 163, 25, 25, 1, 1, 14, 14, 14, 14, 14, 1, 1, 25, 25, 97, 97, 97, 25, 25, 1, 1] 176 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 41, 24, 25, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 580 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280922 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [80, 49, 13, 13, 25, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 25, 25, 80, 80, 80, 80, 80, 25, 25, 1, 1, 7, 7, 7, 1, 1, 25, 25] 176 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41]) total number of confs: 341 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280922 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280922 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280922/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280922/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280922 Building REAL300000280923 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280923' /scratch/stefan/7769901/working/building/REAL300000280923 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280923 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280923/0 /scratch/stefan/7769901/working/building/REAL300000280923 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1291) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1291 `/scratch/stefan/7769901/working/3D/1291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2F)C=C1) `REAL300000280923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280923 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 33, 33, 33, 87, 87, 33, 73, 87, 87, 87, 1, 1, 4, 4, 4, 1, 1, 87, 87, 87, 1, 1] 129 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280923 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 59, 129, 43, 87, 87, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 129, 129, 129, 87, 87, 1, 1, 1, 87, 87] 129 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280923 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280923 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280923/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280923 Building REAL300000280924 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280924' /scratch/stefan/7769901/working/building/REAL300000280924 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280924 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280924/0 /scratch/stefan/7769901/working/building/REAL300000280924 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1292) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1292 `/scratch/stefan/7769901/working/3D/1292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2)C=C1) `REAL300000280924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280924 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 11, 41, 41, 41, 41, 1, 1] 70 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280924 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 70, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 41, 41, 70, 70, 70, 41, 41, 9, 1, 1, 1, 1, 41, 41] 70 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280924 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280924/1 /scratch/stefan/7769901/working/building/REAL300000280924 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1293) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1293 `/scratch/stefan/7769901/working/3D/1293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2)C=C1) `REAL300000280924.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280924 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 23, 23, 23, 38, 38, 38, 38, 38, 38, 1, 1, 4, 4, 4, 1, 1, 38, 38, 38, 38, 1, 1] 70 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280924 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 70, 16, 38, 38, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 38, 38, 70, 70, 70, 38, 38, 1, 1, 1, 1, 38, 38] 70 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280924 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280924 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280924/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280924/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280924 Building REAL300000280925 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280925' /scratch/stefan/7769901/working/building/REAL300000280925 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280925 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280925/0 /scratch/stefan/7769901/working/building/REAL300000280925 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1294) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1294 `/scratch/stefan/7769901/working/3D/1294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1) `REAL300000280925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280925 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 25, 25, 25, 1, 1] 37 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280925 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 37, 7, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 37, 37, 37, 25, 25, 1, 1, 1, 25, 25] 37 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280925 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280925/1 /scratch/stefan/7769901/working/building/REAL300000280925 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1295) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1295 `/scratch/stefan/7769901/working/3D/1295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1) `REAL300000280925.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280925 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 4, 1, 1, 11, 26, 26, 26, 1, 1] 40 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280925 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 40, 5, 26, 26, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 40, 40, 40, 26, 26, 5, 1, 1, 1, 26, 26] 40 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280925 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280925 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280925/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280925/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280925 Building REAL300000280926 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280926' /scratch/stefan/7769901/working/building/REAL300000280926 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280926 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280926/0 /scratch/stefan/7769901/working/building/REAL300000280926 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1296) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1296 `/scratch/stefan/7769901/working/3D/1296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C) `REAL300000280926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280926 none CC1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 4, 10, 10, 4, 9, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 4, 10, 10, 27, 27, 27, 10, 10, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280926 none CC1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 10, 10, 10, 6, 10, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 7, 7, 7, 1, 1, 10, 10, 10] 27 rigid atoms, others: [43, 38, 39, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46, 47]) total number of confs: 67 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280926 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280926/1 /scratch/stefan/7769901/working/building/REAL300000280926 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1297) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1297 `/scratch/stefan/7769901/working/3D/1297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C) `REAL300000280926.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280926 none CC1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 3, 7, 7, 3, 4, 21, 21, 21, 21, 21, 21, 7, 7, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 21, 7, 7, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280926 none CC1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7, 1, 1, 7, 7, 7] 21 rigid atoms, others: [43, 37, 38, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280926 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280926 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280926/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280926/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280926 Building REAL300000280927 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280927' /scratch/stefan/7769901/working/building/REAL300000280927 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280927 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280927/0 /scratch/stefan/7769901/working/building/REAL300000280927 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1298) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1298 `/scratch/stefan/7769901/working/3D/1298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1) `REAL300000280927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280927 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 1, 1] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280927 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 70, 9, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 70, 70, 70, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 41, 41] 70 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280927 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280927/1 /scratch/stefan/7769901/working/building/REAL300000280927 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1299) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1299 `/scratch/stefan/7769901/working/3D/1299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1) `REAL300000280927.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280927 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 4, 4, 4, 1, 1, 46, 46, 46, 46, 46, 46, 46, 1, 1] 76 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280927 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3OCCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 19, 76, 9, 46, 46, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 76, 76, 76, 46, 46, 1, 1, 1, 1, 1, 1, 1, 46, 46] 76 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280927 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280927 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280927/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280927/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280927 Building REAL300000280928 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280928' /scratch/stefan/7769901/working/building/REAL300000280928 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280928 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280928/0 /scratch/stefan/7769901/working/building/REAL300000280928 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1300) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1300 `/scratch/stefan/7769901/working/3D/1300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280928 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 15, 6, 11, 38, 38, 38, 38, 38, 38, 15, 15, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 15, 15, 38, 38, 38, 15, 15, 2, 2, 2, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280928 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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, 6, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 7, 7, 7, 1, 1, 9, 9, 9, 9] 21 rigid atoms, others: [34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280928 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280928/1 /scratch/stefan/7769901/working/building/REAL300000280928 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1301) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1301 `/scratch/stefan/7769901/working/3D/1301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280928.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280928 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 5, 15, 15, 8, 9, 41, 41, 41, 41, 41, 41, 15, 15, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 41, 41, 41, 15, 15, 2, 2, 2, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280928 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 9, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 1, 1, 9, 9, 9, 9] 24 rigid atoms, others: [33, 34, 38, 39, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 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 /scratch/stefan/7769901/working/building/REAL300000280928 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280928 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280928/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280928/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280928 Building REAL300000280929 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280929' /scratch/stefan/7769901/working/building/REAL300000280929 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280929 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280929/0 /scratch/stefan/7769901/working/building/REAL300000280929 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1302) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1302 `/scratch/stefan/7769901/working/3D/1302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C=C2)C=C1) `REAL300000280929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280929 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 11, 25, 25, 25, 25, 1, 1] 41 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280929 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 9, 41, 5, 25, 25, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 25, 25, 41, 41, 41, 25, 25, 5, 1, 1, 1, 1, 25, 25] 41 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280929 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280929/1 /scratch/stefan/7769901/working/building/REAL300000280929 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1303) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1303 `/scratch/stefan/7769901/working/3D/1303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2)C=C1) `REAL300000280929.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280929 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 4, 4, 4, 1, 1, 23, 23, 23, 23, 1, 1] 40 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280929 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 40, 5, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 40, 40, 40, 23, 23, 1, 1, 1, 1, 23, 23] 40 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280929 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280929 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280929/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280929/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280929 Building REAL300000280930 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280930' /scratch/stefan/7769901/working/building/REAL300000280930 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280930 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280930/0 /scratch/stefan/7769901/working/building/REAL300000280930 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1304) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1304 `/scratch/stefan/7769901/working/3D/1304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1) `REAL300000280930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280930 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 4, 1, 1, 26, 26, 26, 26, 1, 1] 39 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280930 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 39, 5, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 39, 39, 39, 26, 26, 1, 1, 1, 1, 26, 26] 39 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280930 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280930/1 /scratch/stefan/7769901/working/building/REAL300000280930 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1305) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1305 `/scratch/stefan/7769901/working/3D/1305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1) `REAL300000280930.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280930 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 4, 4, 4, 1, 1, 11, 27, 27, 27, 27, 1, 1] 43 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280930 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 43, 5, 27, 27, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 43, 27, 27, 5, 1, 1, 1, 1, 27, 27] 43 rigid atoms, others: [32, 33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280930 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280930 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280930/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280930/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280930 Building REAL300000280931 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280931' /scratch/stefan/7769901/working/building/REAL300000280931 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280931 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280931/0 /scratch/stefan/7769901/working/building/REAL300000280931 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1306) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1306 `/scratch/stefan/7769901/working/3D/1306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1) `REAL300000280931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280931 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 11, 25, 25, 25, 25, 25, 1, 1] 41 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280931 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 9, 41, 5, 25, 25, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 25, 25, 41, 41, 41, 25, 25, 5, 1, 1, 1, 1, 1, 25, 25] 41 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280931 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280931/1 /scratch/stefan/7769901/working/building/REAL300000280931 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1307) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1307 `/scratch/stefan/7769901/working/3D/1307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1) `REAL300000280931.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280931 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 4, 1, 1, 26, 26, 26, 26, 26, 1, 1] 42 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280931 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 10, 42, 5, 26, 26, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 26, 26, 42, 42, 42, 26, 26, 1, 1, 1, 1, 1, 26, 26] 42 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280931 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280931 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280931/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280931/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280931 Building REAL300000280932 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280932' /scratch/stefan/7769901/working/building/REAL300000280932 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280932 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280932/0 /scratch/stefan/7769901/working/building/REAL300000280932 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1308) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1308 `/scratch/stefan/7769901/working/3D/1308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280932 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 12, 17, 71, 71, 71, 71, 81, 81, 23, 23, 1, 1, 3, 3, 3, 3, 1, 1, 9, 23, 23, 71, 71, 71, 23, 23, 1, 1] 106 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 42, 25, 26, 31] set([0, 1, 2, 9, 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]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280932 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 23, 13, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 35, 35, 35, 35, 23, 23, 6, 1, 1, 7, 7, 7, 1, 1, 23, 23] 106 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280932 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280932/1 /scratch/stefan/7769901/working/building/REAL300000280932 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1309) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1309 `/scratch/stefan/7769901/working/3D/1309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280932.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280932 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 9, 15, 73, 73, 73, 73, 79, 79, 25, 25, 1, 1, 3, 3, 3, 3, 1, 1, 25, 25, 73, 73, 73, 25, 25, 1, 1] 101 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 25, 26, 31] set([0, 1, 2, 9, 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]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280932 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 25, 25, 37, 37, 37, 37, 25, 25, 1, 1, 7, 7, 7, 1, 1, 25, 25] 101 rigid atoms, others: [33, 34, 38, 39, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280932 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280932 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280932/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280932/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280932 Building REAL300000280933 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280933' /scratch/stefan/7769901/working/building/REAL300000280933 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280933 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280933/0 /scratch/stefan/7769901/working/building/REAL300000280933 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1310) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1310 `/scratch/stefan/7769901/working/3D/1310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1) `REAL300000280933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280933 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 6, 6, 6, 21, 43, 43, 21, 29, 123, 123, 123, 123, 123, 123, 43, 43, 1, 2, 2, 2, 1, 1, 43, 43, 123, 123, 123, 43, 43] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280933 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 7, 7, 7, 1, 1] 123 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280933 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280933 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280933/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280933 Building REAL300000280934 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280934' /scratch/stefan/7769901/working/building/REAL300000280934 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280934 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280934/0 /scratch/stefan/7769901/working/building/REAL300000280934 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1311) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1311 `/scratch/stefan/7769901/working/3D/1311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280934 none COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 50, 50, 34, 39, 159, 159, 159, 159, 171, 171, 50, 50, 4, 4, 4, 1, 1, 1, 50, 50, 159, 159, 159, 50, 50] 171 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280934 none COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [72, 50, 50, 50, 27, 50, 50, 50, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 72, 72, 72, 50, 50, 50, 1, 1, 7, 7, 7, 1, 1] 171 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280934 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280934/1 /scratch/stefan/7769901/working/building/REAL300000280934 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1312) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1312 `/scratch/stefan/7769901/working/3D/1312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280934.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280934 none COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 53, 53, 25, 41, 157, 157, 157, 157, 157, 157, 53, 53, 4, 4, 4, 1, 1, 1, 25, 53, 53, 157, 157, 157, 53, 53] 157 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280934 none COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [63, 53, 53, 53, 29, 53, 53, 53, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 63, 63, 63, 53, 53, 53, 6, 1, 1, 7, 7, 7, 1, 1] 157 rigid atoms, others: [33, 34, 38, 39, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280934 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280934 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280934/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280934/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280934 Building REAL300000280935 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280935' /scratch/stefan/7769901/working/building/REAL300000280935 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280935 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280935/0 /scratch/stefan/7769901/working/building/REAL300000280935 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1313) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1313 `/scratch/stefan/7769901/working/3D/1313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1) `REAL300000280935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280935 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 29, 29, 29, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 4, 4, 4, 1, 1, 69, 69, 69, 1, 1] 113 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280935 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 43, 113, 30, 69, 69, 19, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 69, 69, 113, 113, 113, 69, 69, 1, 1, 1, 69, 69] 113 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280935 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280935 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280935/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280935 Building REAL300000280936 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280936' /scratch/stefan/7769901/working/building/REAL300000280936 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280936 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280936/0 /scratch/stefan/7769901/working/building/REAL300000280936 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1314) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1314 `/scratch/stefan/7769901/working/3D/1314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280936 none CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 15, 31, 31, 17, 21, 81, 81, 81, 81, 81, 81, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 81, 81, 81, 31, 31] 81 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280936 none CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 31, 23, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 31, 31, 31, 17, 31, 31, 1, 1, 7, 7, 7, 1, 1] 81 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280936 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280936/1 /scratch/stefan/7769901/working/building/REAL300000280936 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1315) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1315 `/scratch/stefan/7769901/working/3D/1315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280936.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280936 none CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 11, 27, 27, 11, 19, 71, 71, 71, 71, 71, 71, 27, 27, 2, 2, 2, 1, 1, 1, 11, 27, 27, 71, 71, 71, 27, 27] 71 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280936 none CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 17, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 17, 27, 27, 6, 1, 1, 7, 7, 7, 1, 1] 71 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280936 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280936 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280936/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280936/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280936 Building REAL300000280937 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280937' /scratch/stefan/7769901/working/building/REAL300000280937 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280937 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280937/0 /scratch/stefan/7769901/working/building/REAL300000280937 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1316) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1316 `/scratch/stefan/7769901/working/3D/1316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2F)C=C1) `REAL300000280937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280937 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 93, 93, 93, 71, 93, 93, 93, 1, 1, 4, 4, 4, 1, 1, 93, 71, 93, 1, 1] 145 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280937 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 63, 145, 43, 93, 93, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 145, 145, 145, 93, 93, 1, 1, 1, 93, 93] 145 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280937 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280937 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280937/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280937 Building REAL300000280938 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280938' /scratch/stefan/7769901/working/building/REAL300000280938 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280938 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280938/0 /scratch/stefan/7769901/working/building/REAL300000280938 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1317) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1317 `/scratch/stefan/7769901/working/3D/1317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1) `REAL300000280938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280938 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 4, 4, 4, 1, 1, 10, 40, 40, 40, 40, 40, 1, 1] 71 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280938 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 17, 71, 9, 40, 40, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 71, 71, 71, 40, 40, 9, 1, 1, 1, 1, 1, 40, 40] 71 rigid atoms, others: [33, 34, 35, 36, 37, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280938 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280938/1 /scratch/stefan/7769901/working/building/REAL300000280938 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1318) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1318 `/scratch/stefan/7769901/working/3D/1318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1) `REAL300000280938.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280938 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 41, 1, 1] 73 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280938 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 73, 11, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 73, 73, 73, 41, 41, 1, 1, 1, 1, 1, 41, 41] 73 rigid atoms, others: [32, 33, 34, 35, 36, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280938 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280938 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280938/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280938/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280938 Building REAL300000280939 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280939' /scratch/stefan/7769901/working/building/REAL300000280939 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280939 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280939/0 /scratch/stefan/7769901/working/building/REAL300000280939 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1319) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1319 `/scratch/stefan/7769901/working/3D/1319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280939 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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: [7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 9, 17, 92, 92, 92, 92, 99, 99, 25, 25, 1, 1, 7, 7, 7, 1, 1, 9, 25, 25, 92, 92, 92, 25, 25, 1, 1] 137 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 23, 24, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280939 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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: [62, 25, 25, 25, 25, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 25, 25, 62, 62, 62, 25, 25, 5, 1, 1, 7, 7, 7, 1, 1, 25, 25] 137 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280939 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280939/1 /scratch/stefan/7769901/working/building/REAL300000280939 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1320) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1320 `/scratch/stefan/7769901/working/3D/1320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280939.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280939 none CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 9, 16, 102, 102, 102, 102, 121, 121, 28, 28, 1, 1, 7, 7, 7, 1, 1, 28, 28, 102, 102, 102, 28, 28, 1, 1] 151 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 24, 38, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280939 none CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 28, 28, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 28, 28, 75, 75, 75, 28, 28, 1, 1, 7, 7, 7, 1, 1, 28, 28] 151 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280939 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280939 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280939/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280939/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280939 Building REAL300000280940 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280940' /scratch/stefan/7769901/working/building/REAL300000280940 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280940 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280940/0 /scratch/stefan/7769901/working/building/REAL300000280940 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1321) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1321 `/scratch/stefan/7769901/working/3D/1321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1) `REAL300000280940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280940 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 24, 24, 24, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 4, 4, 4, 1, 1, 10, 42, 42, 42, 42, 42, 42, 1, 1] 73 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280940 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 73, 9, 42, 42, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 73, 73, 73, 42, 42, 9, 1, 1, 1, 1, 1, 1, 42, 42] 73 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280940 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280940/1 /scratch/stefan/7769901/working/building/REAL300000280940 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1322) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1322 `/scratch/stefan/7769901/working/3D/1322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1) `REAL300000280940.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280940 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 24, 24, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 41, 41, 1, 1] 74 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280940 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 74, 14, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 74, 74, 74, 41, 41, 1, 1, 1, 1, 1, 1, 41, 41] 74 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280940 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280940 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280940/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280940/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280940 Building REAL300000280941 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280941' /scratch/stefan/7769901/working/building/REAL300000280941 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280941 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280941/0 /scratch/stefan/7769901/working/building/REAL300000280941 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1323) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1323 `/scratch/stefan/7769901/working/3D/1323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1) `REAL300000280941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280941 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 80, 80, 80, 80, 80, 80, 80, 1, 1, 4, 4, 4, 1, 1, 80, 80, 1, 1] 131 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280941 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 46, 131, 34, 80, 80, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 131, 131, 131, 80, 80, 1, 1, 80, 80] 131 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280941 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280941 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280941/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280941 Building REAL300000280942 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280942' /scratch/stefan/7769901/working/building/REAL300000280942 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280942 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280942/0 /scratch/stefan/7769901/working/building/REAL300000280942 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1324) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1324 `/scratch/stefan/7769901/working/3D/1324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1) `REAL300000280942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280942 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 20, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 4, 4, 4, 1, 1, 7, 36, 36, 36, 36, 1, 1] 63 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280942 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 63, 9, 36, 36, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 63, 63, 63, 36, 36, 9, 1, 1, 1, 1, 36, 36] 63 rigid atoms, others: [33, 34, 35, 36, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280942 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280942/1 /scratch/stefan/7769901/working/building/REAL300000280942 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1325) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1325 `/scratch/stefan/7769901/working/3D/1325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1) `REAL300000280942.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280942 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 26, 26, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 1, 1] 67 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280942 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3NC(=O)OC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 19, 67, 9, 41, 41, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 67, 67, 67, 41, 41, 1, 1, 1, 1, 41, 41] 67 rigid atoms, others: [32, 33, 34, 35, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280942 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280942 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280942/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280942/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280942 Building REAL300000280943 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280943' /scratch/stefan/7769901/working/building/REAL300000280943 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280943 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280943/0 /scratch/stefan/7769901/working/building/REAL300000280943 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1326) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1326 `/scratch/stefan/7769901/working/3D/1326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCS(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000280943 none COC(=O)CCS(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 96, 28, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 96, 96, 96, 46, 46, 28, 28, 4, 1, 1, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280943 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280943 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280943/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280943 Building REAL300000280944 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280944' /scratch/stefan/7769901/working/building/REAL300000280944 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280944 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280944/0 /scratch/stefan/7769901/working/building/REAL300000280944 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1327) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1327 `/scratch/stefan/7769901/working/3D/1327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280944 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 33, 33, 13, 25, 92, 92, 92, 92, 92, 92, 33, 33, 2, 2, 2, 1, 1, 1, 13, 33, 33, 92, 92, 92, 33, 33] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280944 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 33, 33, 33, 33, 33, 33, 6, 1, 1, 7, 7, 7, 1, 1] 92 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280944 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280944/1 /scratch/stefan/7769901/working/building/REAL300000280944 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1328) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1328 `/scratch/stefan/7769901/working/3D/1328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280944.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280944 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 33, 33, 15, 23, 104, 104, 104, 104, 104, 104, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 104, 104, 104, 33, 33] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280944 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 7, 7, 7, 1, 1] 104 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280944 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280944 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280944/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280944/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280944 Building REAL300000280945 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280945' /scratch/stefan/7769901/working/building/REAL300000280945 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280945 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280945/0 /scratch/stefan/7769901/working/building/REAL300000280945 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1329) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1329 `/scratch/stefan/7769901/working/3D/1329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280945 none CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 58, 58, 32, 38, 156, 156, 156, 156, 156, 156, 58, 58, 2, 2, 2, 2, 2, 2, 2, 2, 2, 58, 58, 156, 156, 156, 58, 58] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280945 none CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 7, 7, 7, 1, 1] 156 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280945 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280945 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280945/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280945 Building REAL300000280946 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280946' /scratch/stefan/7769901/working/building/REAL300000280946 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280946 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280946/0 /scratch/stefan/7769901/working/building/REAL300000280946 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1330) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1330 `/scratch/stefan/7769901/working/3D/1330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280946 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 9, 16, 105, 105, 105, 105, 147, 147, 26, 26, 1, 1, 6, 6, 6, 1, 1, 26, 26, 105, 105, 105, 26, 26, 1, 1] 150 rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 40, 25, 26, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280946 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 26, 68, 14, 26, 26, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 26, 26, 68, 68, 68, 26, 26, 1, 1, 7, 7, 7, 1, 1, 26, 26] 150 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280946 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280946/1 /scratch/stefan/7769901/working/building/REAL300000280946 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1331) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1331 `/scratch/stefan/7769901/working/3D/1331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280946.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280946 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 26, 26, 15, 19, 97, 97, 97, 97, 133, 133, 26, 26, 1, 1, 7, 7, 7, 1, 1, 9, 26, 26, 97, 97, 97, 26, 26, 1, 1] 140 rigid atoms, others: [2, 4, 5, 6, 7, 8, 41, 40, 25, 26, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280946 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 26, 68, 26, 26, 26, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 26, 26, 68, 68, 68, 26, 26, 6, 1, 1, 7, 7, 7, 1, 1, 26, 26] 140 rigid atoms, others: [33, 34, 38, 39, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280946 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280946 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280946/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280946/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280946 Building REAL300000280947 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280947' /scratch/stefan/7769901/working/building/REAL300000280947 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280947 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280947/0 /scratch/stefan/7769901/working/building/REAL300000280947 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1332) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1332 `/scratch/stefan/7769901/working/3D/1332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280947 none CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 14, 16, 81, 81, 81, 81, 81, 81, 21, 21, 1, 1, 4, 4, 4, 4, 1, 1, 9, 21, 21, 81, 81, 81, 21, 21, 1, 1] 85 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 25, 26, 31] set([0, 1, 3, 9, 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]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280947 none CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 21, 40, 21, 21, 21, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 21, 21, 40, 40, 40, 40, 21, 21, 6, 1, 1, 7, 7, 7, 1, 1, 21, 21] 85 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280947 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280947/1 /scratch/stefan/7769901/working/building/REAL300000280947 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1333) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1333 `/scratch/stefan/7769901/working/3D/1333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280947.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280947 none CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 15, 90, 90, 90, 90, 90, 90, 23, 23, 1, 1, 4, 4, 4, 4, 1, 1, 23, 23, 90, 90, 90, 23, 23, 1, 1] 94 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 40, 25, 26, 31] set([0, 1, 3, 9, 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]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280947 none CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 13, 38, 13, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 38, 38, 38, 38, 23, 23, 1, 1, 7, 7, 7, 1, 1, 23, 23] 94 rigid atoms, others: [33, 34, 38, 39, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280947 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280947 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280947/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280947/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280947 Building REAL300000280948 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280948' /scratch/stefan/7769901/working/building/REAL300000280948 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280948 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280948/0 /scratch/stefan/7769901/working/building/REAL300000280948 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1334) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1334 `/scratch/stefan/7769901/working/3D/1334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280948 none NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 9, 24, 24, 10, 17, 67, 67, 67, 67, 67, 67, 24, 24, 1, 1, 2, 2, 1, 1, 9, 24, 24, 67, 67, 67, 24, 24, 1, 1] 67 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 24, 25, 38, 28, 29] set([0, 2, 8, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280948 none NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 24, 24, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 24, 24, 24, 24, 24, 24, 5, 1, 1, 7, 7, 7, 1, 1, 24, 24] 67 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280948 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280948/1 /scratch/stefan/7769901/working/building/REAL300000280948 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1335) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1335 `/scratch/stefan/7769901/working/3D/1335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280948.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280948 none NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 15, 65, 65, 65, 65, 65, 65, 23, 23, 1, 1, 2, 2, 1, 1, 23, 23, 65, 65, 65, 23, 23, 1, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 38, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280948 none NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 13, 23, 13, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 7, 7, 7, 1, 1, 23, 23] 65 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280948 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280948 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280948/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280948/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280948 Building REAL300000280949 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280949' /scratch/stefan/7769901/working/building/REAL300000280949 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280949 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280949/0 /scratch/stefan/7769901/working/building/REAL300000280949 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1336) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1336 `/scratch/stefan/7769901/working/3D/1336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280949 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 9, 21, 95, 95, 95, 95, 95, 95, 29, 29, 1, 1, 4, 4, 4, 4, 4, 1, 1, 9, 29, 29, 95, 95, 95, 29, 29, 1, 1] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 41, 23, 24, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280949 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 29, 29, 39, 39, 39, 39, 39, 29, 29, 6, 1, 1, 7, 7, 7, 1, 1, 29, 29] 95 rigid atoms, others: [33, 34, 38, 39, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280949 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280949/1 /scratch/stefan/7769901/working/building/REAL300000280949 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1337) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1337 `/scratch/stefan/7769901/working/3D/1337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280949.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280949 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 9, 16, 91, 91, 91, 91, 94, 94, 28, 28, 1, 1, 5, 5, 5, 4, 4, 1, 1, 28, 28, 91, 91, 91, 28, 28, 1, 1] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 23, 24, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280949 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 28, 28, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 1, 1, 28, 28, 42, 42, 42, 42, 42, 28, 28, 1, 1, 7, 7, 7, 1, 1, 28, 28] 94 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280949 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280949 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280949/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280949/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280949 Building REAL300000280950 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280950' /scratch/stefan/7769901/working/building/REAL300000280950 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280950 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280950/0 /scratch/stefan/7769901/working/building/REAL300000280950 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1338) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1338 `/scratch/stefan/7769901/working/3D/1338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1) `REAL300000280950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280950 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 9, 41, 41, 41, 41, 41, 41, 41, 1, 1] 71 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280950 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 18, 71, 17, 41, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 71, 71, 71, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 41, 41] 71 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280950 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280950/1 /scratch/stefan/7769901/working/building/REAL300000280950 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1339) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1339 `/scratch/stefan/7769901/working/3D/1339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1) `REAL300000280950.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280950 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 4, 4, 4, 1, 1, 47, 47, 47, 47, 47, 47, 47, 1, 1] 76 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280950 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 19, 76, 9, 47, 47, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 76, 76, 76, 47, 47, 1, 1, 1, 1, 1, 1, 1, 47, 47] 76 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280950 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280950 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280950/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280950/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280950 Building REAL300000280951 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280951' /scratch/stefan/7769901/working/building/REAL300000280951 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280951 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280951/0 /scratch/stefan/7769901/working/building/REAL300000280951 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1340) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1340 `/scratch/stefan/7769901/working/3D/1340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=CS1) `REAL300000280951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280951 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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, 11, 1, 11, 1, 1, 1, 7, 7, 7, 19, 44, 44, 19, 29, 139, 139, 139, 139, 185, 185, 44, 44, 1, 1, 1, 11, 11, 11, 44, 44, 139, 139, 139, 44, 44, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 23, 24, 25, 37, 36] set([0, 1, 3, 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]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280951 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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: [102, 102, 44, 102, 44, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 44, 44, 44, 102, 102, 102, 1, 1, 5, 5, 5, 1, 1, 44, 44] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280951 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280951 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280951/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280951 Building REAL300000280952 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280952' /scratch/stefan/7769901/working/building/REAL300000280952 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280952 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280952/0 /scratch/stefan/7769901/working/building/REAL300000280952 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1341) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1341 `/scratch/stefan/7769901/working/3D/1341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280952 none COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 13, 61, 61, 61, 61, 84, 84, 17, 17, 1, 1, 12, 12, 12, 6, 6, 4, 4, 1, 1, 9, 17, 17, 61, 61, 61, 17, 17, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 44, 45, 35, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280952 none COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 29, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 17, 17, 81, 81, 81, 57, 57, 29, 29, 17, 17, 4, 1, 1, 5, 5, 5, 1, 1, 17, 17] 201 rigid atoms, others: [43, 37, 38, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 44, 45]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280952 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280952/1 /scratch/stefan/7769901/working/building/REAL300000280952 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1342) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1342 `/scratch/stefan/7769901/working/3D/1342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280952.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280952 none COCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 13, 65, 65, 65, 65, 104, 104, 17, 17, 1, 1, 22, 22, 22, 5, 5, 3, 3, 1, 1, 17, 17, 65, 65, 65, 17, 17, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 43, 44, 35, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280952 none COCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 17, 17, 97, 97, 97, 53, 53, 33, 33, 17, 17, 1, 1, 5, 5, 5, 1, 1, 17, 17] 201 rigid atoms, others: [36, 37, 41, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280952 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280952 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280952/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280952/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280952 Building REAL300000280953 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280953' /scratch/stefan/7769901/working/building/REAL300000280953 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280953 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280953/0 /scratch/stefan/7769901/working/building/REAL300000280953 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1343) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1343 `/scratch/stefan/7769901/working/3D/1343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280953 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 15, 5, 11, 44, 44, 44, 44, 75, 75, 15, 15, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 15, 15, 44, 44, 44, 15, 15, 2, 2, 2, 1] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 45, 24, 25, 26, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280953 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 26, 26, 26, 15, 15, 15, 15, 6, 1, 1, 7, 7, 7, 1, 1, 15, 15, 15, 15] 75 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280953 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280953 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280953/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280953 Building REAL300000280954 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280954' /scratch/stefan/7769901/working/building/REAL300000280954 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280954 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280954/0 /scratch/stefan/7769901/working/building/REAL300000280954 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1344) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1344 `/scratch/stefan/7769901/working/3D/1344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280954 none CC(C)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 12, 20, 75, 75, 75, 75, 123, 123, 27, 27, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 9, 27, 27, 75, 75, 75, 27, 27, 1, 1] 171 rigid atoms, others: [3, 36, 5, 6, 7, 8, 46, 47, 25, 4, 26, 37] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280954 none CC(C)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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] 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: [59, 43, 59, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 59, 59, 59, 59, 59, 59, 59, 43, 43, 27, 27, 6, 1, 1, 7, 7, 7, 1, 1, 27, 27] 171 rigid atoms, others: [45, 39, 40, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280954 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280954/1 /scratch/stefan/7769901/working/building/REAL300000280954 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1345) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1345 `/scratch/stefan/7769901/working/3D/1345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280954.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280954 none CC(C)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 9, 16, 85, 85, 85, 85, 127, 127, 26, 26, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 26, 26, 85, 85, 85, 26, 26, 1, 1] 173 rigid atoms, others: [3, 36, 5, 6, 7, 8, 45, 46, 25, 4, 26, 37] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280954 none CC(C)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 42, 58, 26, 26, 26, 26, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 26, 26, 58, 58, 58, 58, 58, 58, 58, 42, 42, 26, 26, 1, 1, 7, 7, 7, 1, 1, 26, 26] 173 rigid atoms, others: [43, 38, 39, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280954 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280954 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280954/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280954/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280954 Building REAL300000280955 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280955' /scratch/stefan/7769901/working/building/REAL300000280955 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280955 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280955/0 /scratch/stefan/7769901/working/building/REAL300000280955 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1346) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1346 `/scratch/stefan/7769901/working/3D/1346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2)C=C1) `REAL300000280955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280955 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 11, 25, 25, 25, 25, 1, 1] 41 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280955 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 9, 41, 5, 25, 25, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 25, 25, 41, 41, 41, 25, 25, 5, 1, 1, 1, 1, 25, 25] 41 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280955 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280955/1 /scratch/stefan/7769901/working/building/REAL300000280955 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1347) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1347 `/scratch/stefan/7769901/working/3D/1347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2)C=C1) `REAL300000280955.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280955 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 4, 4, 4, 1, 1, 23, 23, 23, 23, 1, 1] 40 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280955 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 40, 5, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 40, 40, 40, 23, 23, 1, 1, 1, 1, 23, 23] 40 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280955 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280955 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280955/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280955/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280955 Building REAL300000280956 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280956' /scratch/stefan/7769901/working/building/REAL300000280956 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280956 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280956/0 /scratch/stefan/7769901/working/building/REAL300000280956 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1348) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1348 `/scratch/stefan/7769901/working/3D/1348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2F)C=C1) `REAL300000280956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280956 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 84, 84, 31, 84, 84, 84, 1, 1, 4, 4, 4, 1, 1, 84, 84, 71, 84, 1, 1] 130 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280956 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 130, 45, 84, 84, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 84, 84, 130, 130, 130, 84, 84, 1, 1, 1, 1, 84, 84] 130 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280956 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280956 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280956/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280956 Building REAL300000280957 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280957' /scratch/stefan/7769901/working/building/REAL300000280957 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280957 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280957/0 /scratch/stefan/7769901/working/building/REAL300000280957 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1349) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1349 `/scratch/stefan/7769901/working/3D/1349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280957 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 34, 34, 24, 25, 112, 112, 112, 112, 129, 129, 34, 34, 20, 20, 20, 20, 20, 1, 1, 34, 34, 112, 112, 112, 34, 34] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 4, 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]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280957 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 61, 60, 34, 60, 34, 34, 34, 34, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 1, 1, 89, 89, 89, 89, 89, 34, 34, 1, 1, 5, 5, 5, 1, 1] 201 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280957 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280957 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280957/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280957 Building REAL300000280958 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280958' /scratch/stefan/7769901/working/building/REAL300000280958 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280958 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280958/0 /scratch/stefan/7769901/working/building/REAL300000280958 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1350) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1350 `/scratch/stefan/7769901/working/3D/1350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1) `REAL300000280958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280958 none CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 32, 35, 124, 124, 124, 124, 124, 124, 49, 49, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 49, 49, 124, 124, 124, 49, 49, 1] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 42, 7, 34, 25, 33, 27, 26, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280958 none CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 7, 7, 7, 1, 1, 49] 124 rigid atoms, others: [35, 36, 40, 41, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280958 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280958/1 /scratch/stefan/7769901/working/building/REAL300000280958 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1351) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1351 `/scratch/stefan/7769901/working/3D/1351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1) `REAL300000280958.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280958 none CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 1, 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, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 23, 37, 119, 119, 119, 119, 119, 119, 47, 47, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 23, 47, 47, 119, 119, 119, 47, 47, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 43, 25, 33, 27, 26, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280958 none CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)NCC(=O)[O-])C=C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 1, 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, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 47, 47, 47, 47, 47, 47, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 1, 1, 7, 7, 7, 1, 1, 47] 119 rigid atoms, others: [36, 37, 41, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280958 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280958 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280958/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280958/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280958 Building REAL300000280959 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280959' /scratch/stefan/7769901/working/building/REAL300000280959 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280959 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280959/0 /scratch/stefan/7769901/working/building/REAL300000280959 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1352) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1352 `/scratch/stefan/7769901/working/3D/1352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280959 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 9, 12, 53, 53, 53, 53, 101, 101, 15, 15, 1, 1, 20, 20, 20, 20, 20, 12, 12, 1, 1, 9, 15, 15, 53, 53, 53, 15, 15, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 44, 45, 35, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 444 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280959 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 33, 9, 9, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 15, 15, 92, 92, 92, 92, 92, 50, 50, 15, 15, 4, 1, 1, 5, 5, 5, 1, 1, 15, 15] 201 rigid atoms, others: [43, 37, 38, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 44, 45]) total number of confs: 406 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280959 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280959/1 /scratch/stefan/7769901/working/building/REAL300000280959 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1353) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1353 `/scratch/stefan/7769901/working/3D/1353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000280959.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280959 none CCCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 13, 61, 61, 61, 61, 110, 110, 17, 17, 1, 1, 16, 16, 16, 15, 15, 9, 9, 1, 1, 17, 17, 61, 61, 61, 17, 17, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 43, 44, 35, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 443 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280959 none CCCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 35, 17, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 17, 17, 91, 91, 91, 91, 91, 49, 49, 17, 17, 1, 1, 5, 5, 5, 1, 1, 17, 17] 201 rigid atoms, others: [36, 37, 41, 42, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44]) total number of confs: 419 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280959 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280959 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280959/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280959/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280959 Building REAL300000280960 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280960' /scratch/stefan/7769901/working/building/REAL300000280960 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280960 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280960/0 /scratch/stefan/7769901/working/building/REAL300000280960 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1354) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1354 `/scratch/stefan/7769901/working/3D/1354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1) `REAL300000280960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280960 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 23, 23, 11, 15, 61, 61, 61, 61, 61, 61, 23, 23, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 61, 61, 61, 23, 23, 1] 61 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280960 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 23, 23, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 7, 7, 7, 1, 1, 23] 61 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280960 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280960/1 /scratch/stefan/7769901/working/building/REAL300000280960 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1355) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1355 `/scratch/stefan/7769901/working/3D/1355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1) `REAL300000280960.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280960 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 23, 23, 9, 16, 57, 57, 57, 57, 57, 57, 23, 23, 1, 1, 1, 2, 2, 2, 1, 1, 9, 23, 23, 57, 57, 57, 23, 23, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280960 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 23, 23, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 7, 7, 7, 1, 1, 23] 57 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280960 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280960 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280960/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280960/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280960 Building REAL300000280961 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280961' /scratch/stefan/7769901/working/building/REAL300000280961 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280961 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280961/0 /scratch/stefan/7769901/working/building/REAL300000280961 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1356) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1356 `/scratch/stefan/7769901/working/3D/1356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280961 none CC1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 13, 25, 25, 17, 21, 73, 73, 73, 73, 73, 73, 25, 25, 2, 2, 2, 1, 1, 1, 13, 25, 25, 73, 73, 73, 25, 25] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280961 none CC1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 21, 21, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1] 73 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280961 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280961/1 /scratch/stefan/7769901/working/building/REAL300000280961 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1357) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1357 `/scratch/stefan/7769901/working/3D/1357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280961.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280961 none CC1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 36, 36, 22, 26, 94, 94, 94, 94, 94, 94, 36, 36, 2, 2, 2, 1, 1, 1, 36, 36, 94, 94, 94, 36, 36] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280961 none CC1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 25, 25, 36, 36, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 36, 36, 36, 36, 36, 36, 1, 1, 7, 7, 7, 1, 1] 94 rigid atoms, others: [32, 36, 37, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280961 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280961 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280961/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280961/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280961 Building REAL300000280962 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280962' /scratch/stefan/7769901/working/building/REAL300000280962 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280962 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280962/0 /scratch/stefan/7769901/working/building/REAL300000280962 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1358) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1358 `/scratch/stefan/7769901/working/3D/1358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1) `REAL300000280962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280962 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 41, 41, 35, 35, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 1, 1] 61 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280962 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 61, 18, 41, 41, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 61, 61, 61, 41, 41, 1, 1, 1, 41, 41] 61 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280962 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280962/1 /scratch/stefan/7769901/working/building/REAL300000280962 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1359) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1359 `/scratch/stefan/7769901/working/3D/1359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1) `REAL300000280962.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280962 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 31, 31, 31, 39, 39, 35, 35, 39, 39, 39, 1, 1, 4, 4, 4, 1, 1, 11, 39, 39, 39, 1, 1] 59 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280962 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(F)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 59, 11, 39, 39, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 59, 59, 59, 39, 39, 11, 1, 1, 1, 39, 39] 59 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280962 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280962 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280962/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280962/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280962 Building REAL300000280963 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280963' /scratch/stefan/7769901/working/building/REAL300000280963 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280963 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280963/0 /scratch/stefan/7769901/working/building/REAL300000280963 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1360) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1360 `/scratch/stefan/7769901/working/3D/1360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)N2CCC3=CC=CC=C3C2)C=C1) `REAL300000280963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280963 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)N2CCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 29, 29, 29, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 4, 4, 4, 1, 1, 11, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1] 149 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 44, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280963 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)N2CCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 24, 149, 24, 88, 88, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 149, 149, 149, 88, 88, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88] 149 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280963 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280963 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280963/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280963 Building REAL300000280964 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280964' /scratch/stefan/7769901/working/building/REAL300000280964 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280964 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280964/0 /scratch/stefan/7769901/working/building/REAL300000280964 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1361) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1361 `/scratch/stefan/7769901/working/3D/1361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-]) `REAL300000280964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280964 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 3, 9, 27, 27, 9, 16, 63, 63, 63, 63, 63, 63, 27, 27, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 63, 63, 63, 27, 27, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 37, 21, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280964 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 63 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280964 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280964/1 /scratch/stefan/7769901/working/building/REAL300000280964 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1362) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1362 `/scratch/stefan/7769901/working/3D/1362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-]) `REAL300000280964.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280964 none CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 3, 9, 26, 26, 9, 19, 60, 60, 60, 60, 60, 60, 26, 26, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 26, 26, 60, 60, 60, 26, 26, 1] 60 rigid atoms, others: [0, 1, 2, 3, 4, 38, 21, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280964 none CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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: [26, 26, 26, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 7, 7, 7, 1, 1, 26] 60 rigid atoms, others: [32, 36, 37, 7, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280964 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280964 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280964/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280964/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280964 Building REAL300000280965 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280965' /scratch/stefan/7769901/working/building/REAL300000280965 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280965 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280965/0 /scratch/stefan/7769901/working/building/REAL300000280965 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1363) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1363 `/scratch/stefan/7769901/working/3D/1363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1Cl) `REAL300000280965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280965 none CN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 84, 84, 38, 58, 201, 201, 201, 201, 201, 201, 84, 84, 1, 1, 2, 2, 2, 1, 84, 84, 201, 201, 201, 84, 84] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280965 none CN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 13, 13, 1, 1, 84, 84, 84, 84, 84, 84, 1, 1, 6, 6, 6, 1, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280965 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280965 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280965/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280965 Building REAL300000280966 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280966' /scratch/stefan/7769901/working/building/REAL300000280966 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280966 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280966/0 /scratch/stefan/7769901/working/building/REAL300000280966 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1364) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1364 `/scratch/stefan/7769901/working/3D/1364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O) `REAL300000280966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280966 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 15, 17, 89, 89, 89, 89, 105, 105, 29, 29, 1, 1, 1, 4, 4, 2, 2, 2, 1, 29, 29, 89, 89, 89, 29, 29, 1, 4, 4] 105 rigid atoms, others: [0, 1, 2, 3, 4, 37, 21, 22, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280966 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 29, 37, 37, 29, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1, 29, 37, 37] 105 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280966 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280966/1 /scratch/stefan/7769901/working/building/REAL300000280966 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1365) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1365 `/scratch/stefan/7769901/working/3D/1365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O) `REAL300000280966.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280966 none CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 3, 3, 9, 25, 25, 9, 19, 83, 83, 83, 83, 101, 101, 25, 25, 1, 1, 1, 4, 4, 2, 2, 2, 1, 9, 25, 25, 83, 83, 83, 25, 25, 1, 4, 4] 111 rigid atoms, others: [0, 1, 2, 3, 4, 38, 21, 22, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280966 none CN1C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 25, 37, 37, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25, 37, 37] 111 rigid atoms, others: [32, 36, 37, 7, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280966 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280966 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280966/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280966/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280966 Building REAL300000280967 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280967' /scratch/stefan/7769901/working/building/REAL300000280967 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280967 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280967/0 /scratch/stefan/7769901/working/building/REAL300000280967 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1366) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1366 `/scratch/stefan/7769901/working/3D/1366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280967 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 14, 18, 103, 103, 103, 103, 159, 159, 25, 25, 1, 1, 1, 3, 3, 3, 1, 1, 9, 25, 25, 103, 103, 103, 25, 25, 1] 159 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 23, 24, 25, 29, 30] set([0, 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]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280967 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [61, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 25, 61, 61, 61, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25] 159 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280967 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280967/1 /scratch/stefan/7769901/working/building/REAL300000280967 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1367) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1367 `/scratch/stefan/7769901/working/3D/1367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280967.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280967 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 13, 16, 104, 104, 104, 104, 160, 160, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 27, 27, 104, 104, 104, 27, 27, 1] 160 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 24, 25, 38, 29, 30] set([0, 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]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280967 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 63, 63, 63, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 160 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280967 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280967 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280967/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280967/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280967 Building REAL300000280968 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280968' /scratch/stefan/7769901/working/building/REAL300000280968 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280968 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280968/0 /scratch/stefan/7769901/working/building/REAL300000280968 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1368) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1368 `/scratch/stefan/7769901/working/3D/1368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F) `REAL300000280968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280968 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 10, 18, 101, 101, 101, 101, 160, 160, 25, 25, 1, 1, 1, 3, 3, 3, 1, 1, 9, 25, 25, 101, 101, 101, 25, 25, 1] 160 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 23, 24, 25, 29, 30] set([0, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280968 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [60, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 25, 60, 60, 60, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25] 160 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280968 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280968/1 /scratch/stefan/7769901/working/building/REAL300000280968 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1369) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1369 `/scratch/stefan/7769901/working/3D/1369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F) `REAL300000280968.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280968 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 13, 16, 103, 103, 103, 103, 160, 160, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 27, 27, 103, 103, 103, 27, 27, 1] 160 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 24, 25, 38, 29, 30] set([0, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280968 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 59, 59, 59, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 160 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280968 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280968 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280968/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280968/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280968 Building REAL300000280969 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280969' /scratch/stefan/7769901/working/building/REAL300000280969 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280969 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280969/0 /scratch/stefan/7769901/working/building/REAL300000280969 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1370) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1370 `/scratch/stefan/7769901/working/3D/1370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280969 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 17, 21, 113, 113, 113, 113, 155, 155, 29, 29, 1, 1, 1, 4, 4, 4, 1, 1, 9, 29, 29, 113, 113, 113, 29, 29, 1, 2, 2, 2] 155 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 23, 24, 25, 29, 30] set([0, 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: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280969 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [64, 29, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 29, 64, 64, 64, 29, 29, 6, 1, 1, 7, 7, 7, 1, 1, 29, 29, 29, 29] 155 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280969 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280969/1 /scratch/stefan/7769901/working/building/REAL300000280969 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1371) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1371 `/scratch/stefan/7769901/working/3D/1371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280969.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280969 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 14, 17, 119, 119, 119, 119, 169, 169, 29, 29, 1, 1, 1, 4, 4, 4, 1, 1, 29, 29, 119, 119, 119, 29, 29, 1, 2, 2, 2] 169 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 24, 25, 38, 29, 30] set([0, 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: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280969 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 20, 15, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 29, 29, 29, 63, 62, 60, 29, 29, 1, 1, 7, 7, 7, 1, 1, 29, 29, 29, 29] 169 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280969 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280969 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280969/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280969/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280969 Building REAL300000280970 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280970' /scratch/stefan/7769901/working/building/REAL300000280970 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280970 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280970/0 /scratch/stefan/7769901/working/building/REAL300000280970 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1372) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1372 `/scratch/stefan/7769901/working/3D/1372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280970 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 9, 17, 17, 10, 13, 65, 65, 65, 65, 109, 109, 17, 17, 1, 1, 1, 27, 27, 27, 27, 27, 1, 1, 9, 17, 17, 65, 65, 65, 17, 17, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 458 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280970 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 17, 11, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 1, 1, 17, 17, 17, 115, 115, 115, 115, 115, 17, 17, 4, 1, 1, 5, 5, 5, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 402 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280970 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280970/1 /scratch/stefan/7769901/working/building/REAL300000280970 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1373) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1373 `/scratch/stefan/7769901/working/3D/1373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280970.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280970 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 13, 65, 65, 65, 65, 107, 107, 17, 17, 1, 1, 1, 28, 28, 28, 28, 28, 1, 1, 17, 17, 65, 65, 65, 17, 17, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 432 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280970 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 17, 17, 17, 110, 110, 110, 110, 110, 17, 17, 1, 1, 5, 5, 5, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 349 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280970 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280970 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280970/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280970/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280970 Building REAL300000280971 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280971' /scratch/stefan/7769901/working/building/REAL300000280971 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280971 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280971/0 /scratch/stefan/7769901/working/building/REAL300000280971 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1374) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1374 `/scratch/stefan/7769901/working/3D/1374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O) `REAL300000280971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280971 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 9, 17, 78, 78, 78, 78, 130, 130, 23, 23, 1, 1, 1, 4, 4, 2, 2, 2, 1, 1, 9, 23, 23, 78, 78, 78, 23, 23, 1, 4, 4] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280971 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 23, 23, 23, 57, 57, 23, 23, 23, 23, 23, 6, 1, 1, 7, 7, 7, 1, 1, 23, 57, 57] 178 rigid atoms, others: [33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280971 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280971/1 /scratch/stefan/7769901/working/building/REAL300000280971 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1375) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1375 `/scratch/stefan/7769901/working/3D/1375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O) `REAL300000280971.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280971 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 27, 27, 9, 16, 91, 91, 91, 91, 139, 139, 27, 27, 1, 1, 1, 4, 4, 2, 2, 2, 1, 1, 27, 27, 91, 91, 91, 27, 27, 1, 4, 4] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280971 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 64, 64, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27, 64, 64] 180 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280971 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280971 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280971/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280971/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280971 Building REAL300000280972 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280972' /scratch/stefan/7769901/working/building/REAL300000280972 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280972 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280972/0 /scratch/stefan/7769901/working/building/REAL300000280972 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1376) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1376 `/scratch/stefan/7769901/working/3D/1376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=N1) `REAL300000280972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280972 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 15, 16, 74, 74, 74, 74, 74, 74, 26, 26, 1, 1, 2, 2, 2, 1, 26, 26, 74, 74, 74, 26, 26, 1] 74 rigid atoms, others: [0, 1, 2, 3, 4, 34, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280972 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 7, 7, 7, 1, 1, 26] 74 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280972 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280972 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280972/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280972 Building REAL300000280973 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280973' /scratch/stefan/7769901/working/building/REAL300000280973 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280973 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280973/0 /scratch/stefan/7769901/working/building/REAL300000280973 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1377) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1377 `/scratch/stefan/7769901/working/3D/1377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280973 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 35, 35, 22, 25, 91, 91, 91, 91, 91, 91, 35, 35, 2, 2, 2, 1, 1, 1, 35, 35, 91, 91, 91, 35, 35] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280973 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 17, 17, 35, 35, 35, 35, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 7, 7, 7, 1, 1] 91 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280973 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280973/1 /scratch/stefan/7769901/working/building/REAL300000280973 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1378) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1378 `/scratch/stefan/7769901/working/3D/1378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280973.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280973 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 25, 25, 13, 19, 71, 71, 71, 71, 71, 71, 25, 25, 2, 2, 2, 1, 1, 1, 13, 25, 25, 71, 71, 71, 25, 25] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280973 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 17, 20, 25, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1] 71 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280973 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280973 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280973/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280973/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280973 Building REAL300000280974 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280974' /scratch/stefan/7769901/working/building/REAL300000280974 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280974 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280974/0 /scratch/stefan/7769901/working/building/REAL300000280974 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1379) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1379 `/scratch/stefan/7769901/working/3D/1379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCC2=CC=CC=C2)C=C1) `REAL300000280974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280974 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 29, 29, 29, 101, 107, 139, 139, 116, 139, 139, 1, 1, 4, 4, 4, 1, 1, 11, 101, 101, 107, 107, 139, 139, 139, 139, 139, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280974 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 111, 201, 58, 139, 139, 51, 22, 5, 22, 22, 3, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 139, 139, 51, 5, 5, 3, 3, 1, 1, 1, 1, 1, 139, 139] 201 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, 40, 41]) total number of confs: 828 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280974 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280974 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280974/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280974 Building REAL300000280975 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280975' /scratch/stefan/7769901/working/building/REAL300000280975 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280975 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280975/0 /scratch/stefan/7769901/working/building/REAL300000280975 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1380) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1380 `/scratch/stefan/7769901/working/3D/1380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C) `REAL300000280975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280975 none CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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] 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: [10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 9, 17, 113, 113, 113, 113, 125, 125, 29, 29, 1, 1, 1, 10, 10, 10, 10, 1, 29, 29, 113, 113, 113, 29, 29, 1, 2, 2, 2] 153 rigid atoms, others: [2, 4, 5, 6, 7, 39, 24, 25, 26, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280975 none CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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] 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: [77, 77, 29, 77, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 29, 29, 29, 77, 77, 77, 77, 29, 1, 1, 7, 7, 7, 1, 1, 29, 29, 29, 29] 153 rigid atoms, others: [32, 33, 37, 38, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280975 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280975/1 /scratch/stefan/7769901/working/building/REAL300000280975 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1381) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1381 `/scratch/stefan/7769901/working/3D/1381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C) `REAL300000280975.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280975 none CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 9, 20, 109, 109, 109, 109, 133, 133, 27, 27, 1, 1, 1, 12, 12, 12, 12, 1, 9, 27, 27, 109, 109, 109, 27, 27, 1, 2, 2, 2] 177 rigid atoms, others: [2, 4, 5, 6, 7, 40, 24, 25, 26, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280975 none CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 79, 27, 79, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 27, 27, 27, 79, 79, 79, 79, 27, 6, 1, 1, 7, 7, 7, 1, 1, 27, 27, 27, 27] 177 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280975 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280975 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280975/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280975/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280975 Building REAL300000280976 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280976' /scratch/stefan/7769901/working/building/REAL300000280976 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280976 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280976/0 /scratch/stefan/7769901/working/building/REAL300000280976 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1382) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1382 `/scratch/stefan/7769901/working/3D/1382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280976 none CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 25, 25, 13, 21, 75, 75, 75, 75, 75, 75, 25, 25, 2, 2, 2, 1, 1, 1, 13, 25, 25, 75, 75, 75, 25, 25] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280976 none CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 21, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 25, 25, 25, 25, 22, 25, 6, 1, 1, 7, 7, 7, 1, 1] 75 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280976 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280976/1 /scratch/stefan/7769901/working/building/REAL300000280976 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1383) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1383 `/scratch/stefan/7769901/working/3D/1383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280976.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280976 none CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 21, 37, 37, 23, 27, 99, 99, 99, 99, 99, 99, 37, 37, 2, 2, 2, 1, 1, 1, 37, 37, 99, 99, 99, 37, 37] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280976 none CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 27, 37, 37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 37, 37, 37, 37, 27, 37, 1, 1, 7, 7, 7, 1, 1] 99 rigid atoms, others: [32, 36, 37, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280976 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280976 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280976/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280976/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280976 Building REAL300000280977 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280977' /scratch/stefan/7769901/working/building/REAL300000280977 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280977 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280977/0 /scratch/stefan/7769901/working/building/REAL300000280977 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1384) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1384 `/scratch/stefan/7769901/working/3D/1384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1) `REAL300000280977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280977 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 17, 17, 17, 50, 62, 122, 126, 126, 122, 122, 126, 126, 1, 1, 3, 3, 3, 1, 1, 7, 50, 50, 62, 62, 126, 126, 126, 126, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 41, 25, 26, 42, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280977 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 101, 201, 67, 126, 126, 63, 33, 14, 33, 33, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 126, 126, 63, 14, 14, 6, 6, 1, 1, 1, 1, 126, 126] 201 rigid atoms, others: [37, 38, 39, 40, 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, 36, 41, 42]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280977 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280977/1 /scratch/stefan/7769901/working/building/REAL300000280977 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1385) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1385 `/scratch/stefan/7769901/working/3D/1385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1) `REAL300000280977.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280977 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 13, 13, 13, 43, 43, 120, 123, 123, 120, 123, 123, 123, 1, 1, 3, 3, 3, 1, 1, 43, 43, 43, 43, 123, 123, 123, 123, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 298 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280977 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)CCOC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 99, 201, 60, 123, 123, 60, 35, 11, 35, 35, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 123, 123, 11, 11, 11, 11, 1, 1, 1, 1, 123, 123] 201 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]) total number of confs: 846 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280977 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280977 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280977/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280977/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280977 Building REAL300000280978 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280978' /scratch/stefan/7769901/working/building/REAL300000280978 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280978 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280978/0 /scratch/stefan/7769901/working/building/REAL300000280978 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1386) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1386 `/scratch/stefan/7769901/working/3D/1386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280978 none COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 15, 15, 5, 11, 43, 43, 43, 43, 76, 76, 15, 15, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 5, 15, 15, 43, 43, 43, 15, 15, 1, 2, 2, 2] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 42, 7, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280978 none COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 26, 26, 26, 15, 15, 15, 15, 6, 1, 1, 7, 7, 7, 1, 1, 15, 15, 15, 15] 76 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280978 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280978/1 /scratch/stefan/7769901/working/building/REAL300000280978 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1387) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1387 `/scratch/stefan/7769901/working/3D/1387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280978.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280978 none COC1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 9, 49, 49, 49, 49, 83, 83, 15, 15, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 15, 15, 49, 49, 49, 15, 15, 1, 2, 2, 2] 83 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 41, 24, 25, 26] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280978 none COC1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 15, 15, 15, 15, 15, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 15, 15, 15, 27, 27, 27, 15, 15, 15, 15, 1, 1, 7, 7, 7, 1, 1, 15, 15, 15, 15] 83 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280978 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280978 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280978/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280978/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280978 Building REAL300000280979 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280979' /scratch/stefan/7769901/working/building/REAL300000280979 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280979 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280979/0 /scratch/stefan/7769901/working/building/REAL300000280979 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1388) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1388 `/scratch/stefan/7769901/working/3D/1388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280979 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 25, 51, 51, 33, 39, 124, 124, 124, 124, 172, 172, 51, 51, 1, 2, 2, 2, 51, 51, 124, 124, 124, 51, 51, 1] 172 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 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]) total number of confs: 567 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280979 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 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: [51, 51, 51, 51, 71, 71, 51, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 51, 51, 51, 51, 1, 1, 7, 7, 7, 1, 1, 51] 172 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 36]) total number of confs: 219 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280979 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280979 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280979/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280979 Building REAL300000280980 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280980' /scratch/stefan/7769901/working/building/REAL300000280980 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280980 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280980/0 /scratch/stefan/7769901/working/building/REAL300000280980 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1389) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1389 `/scratch/stefan/7769901/working/3D/1389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280980 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 9, 20, 75, 75, 75, 75, 75, 75, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 75, 75, 75, 27, 27, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 23, 24, 36, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280980 none N#CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 7, 7, 7, 1, 1, 27] 75 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280980 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280980/1 /scratch/stefan/7769901/working/building/REAL300000280980 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1390) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1390 `/scratch/stefan/7769901/working/3D/1390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280980.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280980 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 9, 27, 27, 9, 16, 73, 73, 73, 73, 73, 73, 27, 27, 1, 1, 1, 1, 1, 27, 27, 73, 73, 73, 27, 27, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280980 none N#CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 73 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280980 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280980 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280980/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280980/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280980 Building REAL300000280981 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280981' /scratch/stefan/7769901/working/building/REAL300000280981 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280981 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280981/0 /scratch/stefan/7769901/working/building/REAL300000280981 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1391) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1391 `/scratch/stefan/7769901/working/3D/1391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl) `REAL300000280981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280981 none N#CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 24, 24, 9, 18, 68, 68, 68, 68, 68, 68, 24, 24, 1, 1, 1, 1, 1, 9, 24, 24, 68, 68, 68, 24, 24, 1, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 25, 22, 23, 24, 36, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280981 none N#CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 24, 24, 24, 24, 24, 6, 1, 1, 7, 7, 7, 1, 1, 24, 24] 68 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280981 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280981/1 /scratch/stefan/7769901/working/building/REAL300000280981 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1392) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1392 `/scratch/stefan/7769901/working/3D/1392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl) `REAL300000280981.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280981 none N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 9, 27, 27, 9, 16, 67, 67, 67, 67, 67, 67, 27, 27, 1, 1, 1, 1, 1, 27, 27, 67, 67, 67, 27, 27, 1, 1] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280981 none N#CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27, 27] 67 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280981 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280981 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280981/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280981/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280981 Building REAL300000280982 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280982' /scratch/stefan/7769901/working/building/REAL300000280982 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280982 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280982/0 /scratch/stefan/7769901/working/building/REAL300000280982 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1393) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1393 `/scratch/stefan/7769901/working/3D/1393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1) `REAL300000280982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280982 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 4, 4, 4, 1, 1, 8, 35, 35, 35, 35, 35, 1, 1] 60 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280982 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 17, 60, 17, 35, 35, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 60, 60, 60, 35, 35, 9, 1, 1, 1, 1, 1, 35, 35] 60 rigid atoms, others: [33, 34, 35, 36, 37, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280982 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280982/1 /scratch/stefan/7769901/working/building/REAL300000280982 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1394) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1394 `/scratch/stefan/7769901/working/3D/1394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1) `REAL300000280982.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280982 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 4, 4, 4, 1, 1, 38, 38, 38, 38, 38, 1, 1] 60 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280982 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C3COC(=O)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 18, 60, 9, 38, 38, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 60, 60, 60, 38, 38, 1, 1, 1, 1, 1, 38, 38] 60 rigid atoms, others: [32, 33, 34, 35, 36, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280982 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280982 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280982/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280982/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280982 Building REAL300000280983 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280983' /scratch/stefan/7769901/working/building/REAL300000280983 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280983 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280983/0 /scratch/stefan/7769901/working/building/REAL300000280983 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1395) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1395 `/scratch/stefan/7769901/working/3D/1395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280983 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 9, 18, 75, 75, 75, 75, 75, 75, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 9, 25, 25, 75, 75, 75, 25, 25, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280983 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25] 75 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280983 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280983/1 /scratch/stefan/7769901/working/building/REAL300000280983 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1396) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1396 `/scratch/stefan/7769901/working/3D/1396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl) `REAL300000280983.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280983 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 16, 74, 74, 74, 74, 74, 74, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 74, 74, 74, 27, 27, 1] 74 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]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280983 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 74 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280983 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280983 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280983/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280983/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280983 Building REAL300000280984 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280984' /scratch/stefan/7769901/working/building/REAL300000280984 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280984 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280984/0 /scratch/stefan/7769901/working/building/REAL300000280984 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1397) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1397 `/scratch/stefan/7769901/working/3D/1397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2F)C=C1) `REAL300000280984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280984 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 32, 32, 32, 81, 81, 67, 81, 81, 81, 81, 1, 1, 4, 4, 4, 1, 1, 81, 81, 81, 1, 1] 138 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280984 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [138, 138, 138, 138, 138, 56, 138, 43, 81, 81, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 138, 138, 138, 81, 81, 1, 1, 1, 81, 81] 138 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280984 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280984 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280984/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280984 Building REAL300000280985 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280985' /scratch/stefan/7769901/working/building/REAL300000280985 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280985 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280985/0 /scratch/stefan/7769901/working/building/REAL300000280985 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1398) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1398 `/scratch/stefan/7769901/working/3D/1398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F) `REAL300000280985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280985 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 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, 3, 3, 3, 9, 25, 25, 9, 18, 73, 73, 73, 73, 73, 73, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 9, 25, 25, 73, 73, 73, 25, 25, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280985 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1, 25] 73 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280985 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280985/1 /scratch/stefan/7769901/working/building/REAL300000280985 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1399) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1399 `/scratch/stefan/7769901/working/3D/1399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F) `REAL300000280985.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280985 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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 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, 2, 2, 2, 9, 27, 27, 15, 16, 72, 72, 72, 72, 72, 72, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 72, 72, 72, 27, 27, 1] 72 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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280985 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 1, 1, 27] 72 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280985 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280985 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280985/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280985/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280985 Building REAL300000280986 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280986' /scratch/stefan/7769901/working/building/REAL300000280986 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280986 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280986/0 /scratch/stefan/7769901/working/building/REAL300000280986 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1400) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1400 `/scratch/stefan/7769901/working/3D/1400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280986 none CC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 25, 25, 13, 19, 74, 74, 74, 74, 74, 74, 25, 25, 2, 2, 2, 1, 1, 1, 13, 25, 25, 74, 74, 74, 25, 25] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280986 none CC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 17, 17, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1] 74 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280986 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280986/1 /scratch/stefan/7769901/working/building/REAL300000280986 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1401) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1401 `/scratch/stefan/7769901/working/3D/1401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280986.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280986 none CC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 36, 36, 22, 26, 94, 94, 94, 94, 94, 94, 36, 36, 2, 2, 2, 1, 1, 1, 36, 36, 94, 94, 94, 36, 36] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280986 none CC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 17, 17, 36, 36, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 36, 36, 36, 36, 36, 36, 1, 1, 7, 7, 7, 1, 1] 94 rigid atoms, others: [32, 36, 37, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280986 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280986 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280986/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280986/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280986 Building REAL300000280987 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280987' /scratch/stefan/7769901/working/building/REAL300000280987 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280987 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280987/0 /scratch/stefan/7769901/working/building/REAL300000280987 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1402) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1402 `/scratch/stefan/7769901/working/3D/1402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280987 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 54, 54, 31, 41, 148, 148, 148, 148, 148, 148, 54, 54, 1, 2, 2, 2, 1, 1, 54, 54, 148, 148, 148, 54, 54, 1] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280987 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 54, 54, 54, 54, 54, 54, 1, 1, 7, 7, 7, 1, 1, 54] 148 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280987 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280987 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280987/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280987 Building REAL300000280988 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280988' /scratch/stefan/7769901/working/building/REAL300000280988 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280988 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280988/0 /scratch/stefan/7769901/working/building/REAL300000280988 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1403) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1403 `/scratch/stefan/7769901/working/3D/1403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280988 none CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 25, 25, 17, 21, 75, 75, 75, 75, 75, 75, 25, 25, 2, 2, 2, 1, 1, 1, 13, 25, 25, 75, 75, 75, 25, 25] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280988 none CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 7, 7, 7, 1, 1] 75 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280988 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280988/1 /scratch/stefan/7769901/working/building/REAL300000280988 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1404) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1404 `/scratch/stefan/7769901/working/3D/1404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280988.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280988 none CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 21, 37, 37, 21, 27, 97, 97, 97, 97, 97, 97, 37, 37, 2, 2, 2, 1, 1, 1, 37, 37, 97, 97, 97, 37, 37] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280988 none CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 37, 37, 37, 37, 37, 37, 1, 1, 7, 7, 7, 1, 1] 97 rigid atoms, others: [32, 36, 37, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280988 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280988 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280988/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280988/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280988 Building REAL300000280989 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280989' /scratch/stefan/7769901/working/building/REAL300000280989 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280989 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280989/0 /scratch/stefan/7769901/working/building/REAL300000280989 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1405) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1405 `/scratch/stefan/7769901/working/3D/1405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1) `REAL300000280989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280989 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 71, 137, 22, 22, 1, 1, 4, 4, 4, 1, 1, 9, 22, 22, 71, 71, 137, 137, 22, 22, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 41, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280989 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 44, 54, 44, 44, 9, 44, 5, 22, 22, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 14, 1, 1, 22, 22, 44, 44, 44, 22, 22, 5, 1, 1, 8, 8, 14, 14, 1, 1, 22, 22] 201 rigid atoms, others: [32, 33, 38, 39, 12, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280989 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280989/1 /scratch/stefan/7769901/working/building/REAL300000280989 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1406) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1406 `/scratch/stefan/7769901/working/3D/1406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1) `REAL300000280989.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280989 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 77, 125, 25, 25, 1, 1, 4, 4, 4, 1, 1, 25, 25, 77, 77, 125, 125, 25, 25, 1, 1] 186 rigid atoms, others: [5, 7, 8, 9, 10, 11, 40, 39, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 539 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280989 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=C(CCCl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 51, 73, 51, 51, 9, 51, 5, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 1, 1, 25, 25, 51, 51, 51, 25, 25, 1, 1, 8, 8, 13, 13, 1, 1, 25, 25] 186 rigid atoms, others: [32, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280989 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280989 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280989/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280989/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280989 Building REAL300000280990 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280990' /scratch/stefan/7769901/working/building/REAL300000280990 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280990 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280990/0 /scratch/stefan/7769901/working/building/REAL300000280990 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1407) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1407 `/scratch/stefan/7769901/working/3D/1407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000280990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280990 none CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 3, 3, 3, 5, 11, 11, 5, 9, 34, 34, 34, 34, 34, 34, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 34, 34, 34, 11, 11] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 30, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280990 none CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=O)[N-]C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 7, 7, 7, 1, 1] 34 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280990 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280990 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280990/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280990 Building REAL300000280991 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280991' /scratch/stefan/7769901/working/building/REAL300000280991 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280991 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280991/0 /scratch/stefan/7769901/working/building/REAL300000280991 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1408) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1408 `/scratch/stefan/7769901/working/3D/1408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CN=C2C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280991 none CC1=CC2=CC=CN=C2C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 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, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 7, 7, 25, 47, 47, 30, 34, 116, 116, 116, 116, 116, 116, 47, 47, 1, 2, 2, 2, 1, 1, 1, 1, 47, 47, 116, 116, 116, 47, 47, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 33, 27, 42, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280991 none CC1=CC2=CC=CN=C2C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 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, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 7, 7, 7, 1, 1, 47] 116 rigid atoms, others: [35, 36, 40, 41, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280991 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280991/1 /scratch/stefan/7769901/working/building/REAL300000280991 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1409) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1409 `/scratch/stefan/7769901/working/3D/1409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CN=C2C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280991.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280991 none CC1=CC2=CC=CN=C2C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 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, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 40, 40, 27, 33, 110, 110, 110, 110, 110, 110, 40, 40, 1, 2, 2, 2, 1, 1, 1, 1, 21, 40, 40, 110, 110, 110, 40, 40, 1] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 43, 33, 27, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280991 none CC1=CC2=CC=CN=C2C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 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, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 1, 7, 7, 7, 1, 1, 40] 110 rigid atoms, others: [36, 37, 41, 42, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280991 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280991 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280991/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280991/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280991 Building REAL300000280992 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280992' /scratch/stefan/7769901/working/building/REAL300000280992 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280992 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280992/0 /scratch/stefan/7769901/working/building/REAL300000280992 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1410) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1410 `/scratch/stefan/7769901/working/3D/1410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000280992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280992 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 1, 1, 4, 4, 4, 1, 1, 34, 34, 1, 1] 54 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280992 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 54, 16, 34, 34, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 54, 54, 54, 34, 34, 1, 1, 34, 34] 54 rigid atoms, others: [12, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280992 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280992/1 /scratch/stefan/7769901/working/building/REAL300000280992 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1411) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1411 `/scratch/stefan/7769901/working/3D/1411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000280992.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280992 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 1, 1, 4, 4, 4, 1, 1, 9, 36, 36, 1, 1] 55 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280992 none O=C([O-])CNC(=O)C1=CC=C(NS(=O)(=O)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 17, 55, 9, 36, 36, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 55, 55, 55, 36, 36, 9, 1, 1, 36, 36] 55 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280992 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280992 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280992/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280992/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280992 Building REAL300000280993 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280993' /scratch/stefan/7769901/working/building/REAL300000280993 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280993 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280993/0 /scratch/stefan/7769901/working/building/REAL300000280993 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1412) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1412 `/scratch/stefan/7769901/working/3D/1412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1) `REAL300000280993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280993 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 23, 23, 10, 14, 55, 55, 55, 55, 55, 55, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 23, 55, 55, 55, 23, 23, 1, 1, 1, 1, 1] 55 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280993 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 6, 6, 6, 1, 1, 23, 23, 23, 23, 23] 55 rigid atoms, others: [32, 36, 37, 6, 7, 8, 9, 10, 11, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280993 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280993/1 /scratch/stefan/7769901/working/building/REAL300000280993 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1413) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1413 `/scratch/stefan/7769901/working/3D/1413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1) `REAL300000280993.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280993 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 6, 12, 12, 6, 9, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 12, 12, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280993 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 7, 7, 7, 1, 1, 12, 12, 12, 12, 12] 35 rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280993 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280993 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280993/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280993/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280993 Building REAL300000280994 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280994' /scratch/stefan/7769901/working/building/REAL300000280994 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280994 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280994/0 /scratch/stefan/7769901/working/building/REAL300000280994 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1414) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1414 `/scratch/stefan/7769901/working/3D/1414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2[N+](=O)[O-])C=C1) `REAL300000280994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280994 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 25, 25, 25, 1, 1] 42 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280994 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC(F)=CC=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 13, 42, 5, 25, 25, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 42, 42, 42, 25, 25, 1, 1, 1, 25, 25] 42 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280994 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280994 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280994/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280994 Building REAL300000280995 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280995' /scratch/stefan/7769901/working/building/REAL300000280995 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280995 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280995/0 /scratch/stefan/7769901/working/building/REAL300000280995 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1415) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1415 `/scratch/stefan/7769901/working/3D/1415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])C=C1) `REAL300000280995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280995 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 1, 1, 25, 25, 25, 1, 1] 43 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280995 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 43, 5, 25, 25, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 43, 43, 43, 25, 25, 1, 1, 1, 25, 25] 43 rigid atoms, others: [32, 33, 34, 12, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280995 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280995 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280995/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280995 Building REAL300000280996 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280996' /scratch/stefan/7769901/working/building/REAL300000280996 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280996 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280996/0 /scratch/stefan/7769901/working/building/REAL300000280996 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1416) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1416 `/scratch/stefan/7769901/working/3D/1416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280996 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 27, 27, 15, 20, 83, 83, 83, 83, 137, 137, 27, 27, 1, 1, 1, 3, 3, 3, 1, 1, 13, 27, 27, 83, 83, 83, 27, 27, 2, 2, 2, 1] 137 rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 23, 24, 25, 29, 30] set([0, 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]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280996 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [51, 21, 17, 27, 27, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 27, 27, 27, 51, 51, 51, 27, 27, 6, 1, 1, 7, 7, 7, 1, 1, 27, 27, 27, 27] 137 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280996 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280996/1 /scratch/stefan/7769901/working/building/REAL300000280996 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1417) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1417 `/scratch/stefan/7769901/working/3D/1417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1) `REAL300000280996.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280996 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 39, 39, 24, 28, 123, 123, 123, 123, 185, 185, 39, 39, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 123, 123, 123, 39, 39, 2, 2, 2, 1] 185 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 23, 24, 25, 29, 30] set([0, 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]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280996 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 25, 17, 39, 39, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 1, 1, 39, 39, 39, 69, 69, 69, 39, 39, 1, 1, 7, 7, 7, 1, 1, 39, 39, 39, 39] 185 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280996 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280996 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280996/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280996/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280996 Building REAL300000280997 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280997' /scratch/stefan/7769901/working/building/REAL300000280997 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000280997 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280997/0 /scratch/stefan/7769901/working/building/REAL300000280997 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1418) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1418 `/scratch/stefan/7769901/working/3D/1418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280997 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 13, 69, 69, 69, 69, 100, 100, 17, 17, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 5, 17, 17, 69, 69, 69, 17, 17, 1, 2, 2, 2] 100 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 24, 25, 26, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280997 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 17, 17, 17, 44, 44, 44, 17, 17, 17, 17, 6, 1, 1, 7, 7, 7, 1, 1, 17, 17, 17, 17] 100 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280997 /scratch/stefan/7769901/working /scratch/stefan/7769901 mkdir: created directory `1' /scratch/stefan/7769901/working/building/REAL300000280997/1 /scratch/stefan/7769901/working/building/REAL300000280997 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 1 (index: 1419) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1419 `/scratch/stefan/7769901/working/3D/1419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C) `REAL300000280997.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000280997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280997 none COC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 9, 73, 73, 73, 73, 106, 106, 17, 17, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 17, 17, 73, 73, 73, 17, 17, 1, 2, 2, 2] 106 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 41, 24, 25, 26, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280997 none COC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 17, 17, 17, 39, 39, 39, 17, 17, 17, 17, 1, 1, 7, 7, 7, 1, 1, 17, 17, 17, 17] 106 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280997 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280997 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 1: /scratch/stefan/7769901/working/building/REAL300000280997/1.* 0: /scratch/stefan/7769901/working/building/REAL300000280997/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280997 Building REAL300000280998 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280998' /scratch/stefan/7769901/working/building/REAL300000280998 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280998 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280998/0 /scratch/stefan/7769901/working/building/REAL300000280998 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1420) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1420 `/scratch/stefan/7769901/working/3D/1420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000280998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280998 none CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 55, 55, 25, 37, 138, 138, 138, 138, 138, 138, 55, 55, 1, 2, 2, 2, 1, 1, 2, 55, 55, 138, 138, 138, 55, 55, 1] 276 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 38, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280998 none CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 34, 55, 55, 55, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 1, 1, 55, 55, 55, 55, 55, 55, 110, 1, 1, 7, 7, 7, 1, 1, 55] 276 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280998 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280998 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280998/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280998 Building REAL300000280999 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000280999' /scratch/stefan/7769901/working/building/REAL300000280999 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000280999 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000280999/0 /scratch/stefan/7769901/working/building/REAL300000280999 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1421) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1421 `/scratch/stefan/7769901/working/3D/1421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CNN=C2)C=C1) `REAL300000280999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000280999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000280999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280999 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CNN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 1, 1, 4, 4, 4, 1, 1, 22, 22, 22, 1, 1] 37 rigid atoms, others: [5, 7, 8, 9, 10, 11, 20, 21, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000280999 none O=C([O-])CNC(=O)C1=CC=C([N-]S(=O)(=O)C2=CNN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 11, 41, 7, 24, 24, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 24, 24, 41, 41, 41, 24, 24, 1, 1, 1, 24, 24] 41 rigid atoms, others: [12, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000280999 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000280999 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000280999/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000280999 Building REAL300000281000 mkdir: created directory `/scratch/stefan/7769901/working/building/REAL300000281000' /scratch/stefan/7769901/working/building/REAL300000281000 /scratch/stefan/7769901/working /scratch/stefan/7769901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000281000 mkdir: created directory `0' /scratch/stefan/7769901/working/building/REAL300000281000/0 /scratch/stefan/7769901/working/building/REAL300000281000 /scratch/stefan/7769901/working /scratch/stefan/7769901 Protomer 0 (index: 1422) Found valid previously generated 3D confromation in /scratch/stefan/7769901/working/3D/1422 `/scratch/stefan/7769901/working/3D/1422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1) `REAL300000281000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000281000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769901/working/building/REAL300000281000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000281000 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 23, 52, 52, 33, 35, 157, 157, 157, 157, 172, 172, 52, 52, 1, 9, 9, 9, 1, 1, 52, 52, 157, 157, 157, 52, 52] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 25, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000281000 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)NCC(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 52, 91, 52, 52, 52, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 52, 91, 91, 91, 52, 52, 1, 1, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 36, 37, 11, 12, 13, 14, 15, 16, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769901/working/building/REAL300000281000 /scratch/stefan/7769901/working /scratch/stefan/7769901 Finished preparing REAL300000281000 Recording results /scratch/stefan/7769901/working /scratch/stefan/7769901 Appending to /scratch/stefan/7769901/finished/xaaaaku.* 0: /scratch/stefan/7769901/working/building/REAL300000281000/0.* Removing working files in /scratch/stefan/7769901/working/building/REAL300000281000 /scratch/stefan/7769901 Compressing combined databse files /scratch/stefan/7769901/finished/xaaaaku.db2.gz /scratch/stefan/7769901/finished/xaaaaku.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769901/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769901/working/3D/1423' removed directory: `/scratch/stefan/7769901/working/3D' `/scratch/stefan/7769901/working/protonate' -> `/scratch/stefan/7769901/archive' `/scratch/stefan/7769901/working/input-smiles.ism' -> `/scratch/stefan/7769901/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769901/working/building' rmdir: removing directory, `/scratch/stefan/7769901/working' ls: No match. ls: No match.